First thing, SteveinMD, you may or may not be correct. Newer battery switches are 'make before break' types. Old ones, such as found on anything with an Atomic Four are probably NOT make before break switches.
Now then, with that out of the way, the next thing I'd like to know is what kind of batteries are installed? Are they deep cycle or starting batteries? If they're the ones taunted as being able to do both, get rid of them as soon as you can afford it! Combination batteries all have one thing in common: they can't do either job very well. They don't have many cranking amps, and they don't have many storage minutes, making them the worst of all worlds. If they are starter batteries, (normal automotive type) then they really don't like being run down. The lead plates in a starter battery are very thin, which gives them the ability to provide a lot of amps for a short time. A deep cycle battery, conversely, has thick plates which don't like huge loads (like starter motors, bow thrusters, electric winches, etc.) They want to be discharged at a fairly low, consistent rate. Doing otherwise will kill them. Likewise, long slow loads on a starter battery will kill it in short order. You might (MIGHT!) get five or six deep discharges on a starter battery before those thin plates short out because they've warped.
Now then, on to the alternator. I know this sounds simplistic, but is the belt snug? It's been years since I had an Atomic Four, but as I recall, the fan belt went from the crankshaft to the water pump and then to the alternator. The adjustment for belt tightness is on the alternator. Check the belt, make sure there are no little chunks missing, no cracks, or rubber debris under the engine, alternator, etc. The belt should be snug, not high-e guitar string tight. All that will accomplish is wearing out the bearings in the alternator and water pump. Pick the longest piece of belt, again it's been years, but I think it is the one between the alternator and the engine pulley and push on it with your thumb. You should get less than a half inch of movement, pushing in the dead center of the belt. If not, snug it up a bit.
To accomplish this, take a look at the alternator. It will be pivot mounted in one place to the engine block. The other side will have an adjustment bracket with a slot cut in it. Moving the alternator away from the engine should tighten it up. If you have no adjustment left, (common in a belt with over two years of use), you need to replace it before you even consider changing out the alternator. If the belt is too loose to turn the alternator pulley, it's not going to charge, period.
Okay. The belt is in acceptable shape and snug. Next thing is to take a very hard look at the wires connected to the alternator. I'm operating on old memory again, but as I recall, the Atomic Four's alternator uses an external regulator. You can tell by looking at the back of the alternator. If more than one wire is coming off of it, you have a regulator somewhere. More on that in a moment or two.
If your alternator has one nice big wire coming out of it, then the previous owner did a good thing and put a modern alternator on. (More on that, too.)
In any event, the next thing is universal. If you don't have a DVM (digital volt meter) go and get one. If you have a Harbor Freight close, they have a very, very good one for about $40 bucks. I think Northern Tool has them, too. Last choice is Radio Shack. Don't bother with the cheap ones. Get one that at least has an automatic shut off, or plan on carrying a goodly supply of 9V batteries, because you'll inevitably leave it on and the next time you need it, it won't work...(Experience). Last bit of advice on buying a meter: don't by one of the really expensive ones at an electrical or electronic supply house like a Fluke. You don't need anything that fancy, and you're paying a bundle for the name.
Okay, you've got your new meter. Put it in the DC VOLTs mode. If you're lucky, it'll say DC Volts. If not, look for something that looks like an equal sign ( = ) with a broken, dotted STRAIGHT line above it. That's to make them universal worldwide. For people who can't read... The other thing will be an equal sign with a squiggle line over it ( ~ ). That's AC volts.
Plug the meter leads in. The red lead goes into the VOLTS AC/DC hole. It will usually have a red circle around it to make it easy to find. The black lead will plug into the hole that has a ground symbol. That will look kind of like an upside down christmas tree, and be circled in black. The third hole will say A/MA. That's Amps or Milliamps. That gets useful when you get a little more familiar with troubleshooting your electrical circuit. The A/MA part of the meter will measure either 3 amps or 20 amps. It'll tell you what the maximum input is. If it says 20 amps, be advised this is for a very short time. The built-in shunt resistor in the meter can't dissipate 20 amps very long before something starts melting.
Okay, you have your brandy new meter. What to do with it? First things first. Measure across your batteries with the main switch OFF. As was mentioned, they should read about 12.7 volts DC. BTW, if you have a battery charger, make sure it's off and then wait at least 30 minutes before you check the battery voltage. Plenty of time for a cup of coffee. (NO rum--no yet, anyway.)
Let's assume that the batteries have 12+ volts on them. Both of them. If one is more than .2 volts different, the lower battery may be sick. Not dead, perhaps, but sick. And they only get sicker with time.
Now it's time to do some serious trouble shooting. Turn the battery switch to whichever battery had the higher voltage. If they're the same, it doesn't matter which one you choose. Start the engine, and run the engine up to about 1200-1500 RPM. The reason for this is to make sure you've reached the charging threshold. Most alternators really don't put out much at the usual 700-900 RPM idle speed.
With the engine running at 1200+ RPM, you should see about 13.6 volts on the batteries. You might see as much as 14.4 volts. Any higher than that, and you have a problem, at any time. Shut things down or you'll start melting things like the battery cables and/or the battery posts.
If you have 13.4 to 14.4 volts at the battery, the charging system is (probably) working properly.
If the voltage is below 13.4 volts, or if it didn't change or went down, your charging system isn't working.
Next step. We're assuming the battery voltage remained the same or dropped. Connect the black lead of the meter to the engine block or the alternator itself, even better. Pick a bolt, bracket, etc., with no paint on it. The meter can't read through paint!
With the engine still running, connect the red lead of the meter to the biggest wire leading away from the alternator. This is the charging lead and it is (probably) connected to the COM(mon) connection on the battery switch. If the voltage there is 13.4+ Volts, the alternator is working, and your problem is a bad battery cable, or a bad charging lead. Look hard at the charging lead. It should be a large wire. In the case of electricity, ignore the yard dogs and manufacturers; size counts, and bigger is better!
If the wire or the connectors look like they've gotten hot (discolored, melted), then they probably have. That's a good indication that the wire from the alternator is too bloody small. I know people will beat up on me for this, but I won't run anything smaller than 8 gauge wire from the alternators to the battery/battery switch. 6 ga. is better and 4 ga. is better still. Large wire means less resistance, and less resistance means less heat for one thing, and less 'voltage drop'.
Now then, let's assume that the voltage at the alternator, with the engine running, is the same as the batteries. Time to dig deeper into the mysteries of your charging system.
Shut the engine down. The next thing may involve tugging on wire bundles and harnesses, and you don't need the engine for that.
Let's go back to basics first. Turn your battery switch to OFF. Take another very hard look at your battery cables. If they are nasty-green or gooey white, you've got a corrosion problem! Don't assume anything here unless you've already done this. Get yourself one of the little battery terminal wire brushes at your local auto parts house. They have a little bottle brush, and an internal brush. Disconnect the ground leads (That's the minus [ - ] side of the batteries.) Stuff the bottle brush into the cable leads and spin it until the connectors are shiny inside. Then use the internal brush and put it on the battery terminal and turn it until the metal is shiny. LEAVE THE GROUNDS DISCONNECTED!
Now disconnect the positive ( + ) side of the batteries, and clean those terminals and battery posts. When the terminals and posts are all nice and shiny, you can hook them back up, positive sides first. Be careful the wrench (not pliers, not channel locks or vice grips, please!) doesn't connect between the posts on the battery or you will get your first experience in arc welding, and probably get a nasty burn in the process.
This is a note: If, by some chance, your batteries have bolts with wingnuts on them, take the wingnuts and throw them overboard right now, for two reasons: the first one is common sense! Wingnuts, by their nature, like to loosen themselves up. The second one is that the ABYC and therefore the Coast Guard now frowns very highly on wingnuts for battery connections. Just toss them overboard and go by new nuts and lockwashers.
Make sure that the battery connections, whether they are terminal posts or studs with NUTS are tight. Don't get carried away. They don't have to be torqued to 75 foot pounds or something. Tight. Just average tight will work fine.
When you're done putting the connections back together, slather or spray a corrosion blocker of some kind on the battery terminals. Those little red and green felt gadgets they sell at the auto parts house also work well. Personally, I put a liberal coat of Corrosion Block on everything. It's thin and wicks up into the wire nicely. The greasy stuff is okay, but messy and seems to get onto everything within fifty yards of where you put it.
Now take a hard look at the battery switch terminals, and under them. Do they look like they've gotten hot? If so, toss the switch. If not, we'll do one more test, then assume the switch is okay. With the battery switch in the OFF position, put your meter in the OHMS mode. (That's the horseshoe looking symbol). Set it for the lowest range the meter has. For an auto-ranging meter, it'll be fine. Measure the four terminals from one to the other. (That's a few little tests.) It should read open, or whatever it was showing before you connected the meter leads. If it shows a reading at all or says 0.00, then the switch is bad.
Next, switch the switch to 1 and connect your meter from the connector marked 1 to the connector marked COM. The meter should read 0 ohms or thereabouts. You can take the meter leads and touch them together to find out what the leads measure. The test we're doing now should be just about the same reading. If the meter give you a reading, say 20 ohms or something, the switch is a high-resistance short, and is probably bad.
Check the switch in position 2 to COM. Same holds true. If you see anything much more than the reading from the leads only, the switch is probably shot.
Now, then. You may find a another small connection on the back of the battery switch. It may be labled "Field" or "Safety". If this isn't connected, never, never, never, never switch from Battery 1 to 2 or Both with the engine running. This will blow up the alternator in less time than it takes to say it. (It sounds like this is what you probably did, btw.)
Okay. The battery switch and all of its connections seem good. You've snugged the nuts up. Put it back where it was. Time to head for the alternator again.
Take a look at the back of the alternator. If it has just one nice big wire running from it, it has an internal regulator. (It also won't care about switching the battery switch with the engine running, because the Field winding gets it's voltage from the one wire that is connected to the battery.)
If, after all of this, you have one wire coming out of the alternator, and the voltage doesn't read 13.6 volts with the engine running, the alternator is bad. I'll explain changing it in a bit, and talk about where to get a new one while I'm at it.
If the alternator has more than one big wire, it'll likely have one big wire and two or three small wires. These little wires go off to the voltage regulator. Look around your engine room, and you'll probably find a little black metal box that is about two and a half inches wide, three or four inches long and about two or three inches tall with 3 wires attached. That's your voltage regulator. It also might (not likely, but might) be a black epoxy block with 3 wires attached. That's an electronic regulator, probably a Chrysler automotive unit, and is something to cast an evil eye on. They don't like being mistreated or heat.
If your regulator is the black (or maybe silver or blue) metal can type, it's a Ford style, and they are cheap. If your alternator isn't putting out, change the regulator first. It's cheap. Or...
Here's my real recommendation if you have the original Atomic 4 alternator. Disconnect the positive sides of your batteries to be absolutely safe, disconnect the wires from the back of the alternator, then remove the bolts that are holding the alternator to the engine. Take the belt with you, along with the alternator, to your local NAPA dealer. The reason I'm recommending them is because they have a nice picture book that shows pictures of the alternators they sell, their amp output and physical size. If you go to Advance or one of those places, chances are you'll walk out frustrated and without a replacement part, because they have no way of eyeballing the alternator in a book.
Tell the parts guy you what you're doing. You're replacing an antique alternator, and want a one-wire alternator that is the same size. Let him know you're working on a boat, but that you DO NOT WANT a 'marine alternator'. The simple truth is, they aren't marinized. They don't have stainless bearings, they aren't any better than an automotive unit, and they cost between two and three times as much! If your engine room is dry (and it should be), an automotive unit will last just as long as the more expensive marine units.
I'm working from memory again, but it seems to me that the stock Atomic 4 alternator put out a puny 30 or 35 amps. Select an alternator that puts out at least 50 amps. Some of them go as high as 120 amps, but they usually won't fit without jumping through a few hoops, so choose one that is physically about the same size and has about the same sized pully (diameter!). Make sure the 'pitch' of the pulley is the same. That's why you took the belt with you. While you're at it. Replace the belt unless it's new. Buy one anyway. They always go out when you are heading back into a tight port and it's pouring down rain. Always. Every time. Ask me. Been there, done that. More than once.
As I recall, there is a late 1970's - early 1980's GM alternator that fits right in. A buddy of mine did it, and he said that all he had to do was add a couple of flat washers for spacers to get the pulleys to line up.
Anyway, take your shiny new alternator back to the boat and get it physically installed where the old one was. Take a ruler or other real straight edge, (No, not that piece of scrap teak), and place it vertically across the big engine pully or better, the water pump pulley, which is probably the same thickness. The new alternator's pulley has to be parallel to the other two pulleys or you'll wear belts out in just a couple of hours. If it's within a 1/16 inch, you're good to go. If not, you might have to use some flat washers to shim the pulley until it is straight and parallel. When you're doing this, make sure the attachment bolts are very snug. Alternators like to droop a bit when things are loose.
When you're satisfied that the pulleys are lined up, put the belt on and snug it up. Sometimes you can do this by just pulling the alternator away from the engine by hand, but usually you have to put a pry-bar of some kind in to get the leverage you need. Again, it doesn't have to be 'E' string tight, just hard to push with your thumb. Tighten everything up, and you're ready to wire the beast.
On the back of your shiny new alternator is a 5/16, 3/8 or some metric equivalent nut on an insulated stud. It's usually a copper colored stud. That's your sense/output connection. It may say BAT or ( + ), but that's it. Connect a nice big, heavy wire between that and the COM on your battery switch. Voila! You're finished.
Reconnect your batteries, switch one (or both) of them on, and start the engine. Check the voltage across the battery. It should be 13.6 or there abouts, or maybe as much as 14.4 if it's a really good alternator. That's it. You're done.
(I just replaced my very-very expensive Volvo 35 amp alternator with a one-wire GM 73 amp unit for about $45 bucks. Volvo wanted over $300. The whole job took me three hours, start to finish.)
Now, after a job very well done, it's time to break out the rum and celebrate. Let me tell you a good one! Get yourself a bottle of Bacardi LIMON rum, a six pack of Minutemade Limeade and some club soda. Take a nice stovepipe glass, fill it with cracked ice. Dump in a shot (or so!) of LIMON rum, add the limeade until the glass is about 2/3 full. Fill the glass the rest of the way with Club Soda and you have an Island Breeze. Named after the boss's boat, and approved by none other than Joachim Bacardi (one of our previous neighbors in Miami). I think you'll find that my bud Joachim is marketing something suspiciously like my drink now.
Anyway, take your drink, head for the cockpit, and give yourself a well earned pat on the back and celebrate. You're now an expert!
I know I was long winded, but I wanted to make sure everyone can use this. It can be abridged, and it doesn't take long the second time around.
Good luck. If this hasn't helped, let me know, and we can exchange phone numbers--I'll try and talk you through it.
BTW, I've been boating for nearly a half century (Ye gods!), and have a BSEE, so this is in my back yard.
Later,
Cap'n Gary
S/V Island Breeze, 56' semi-custom cutter