Wow! Can't resist chiming in on this one ....
Two key points are rattling around here, but are being missed, probably because we all have diffeent boats with different setups.
First - if your boat is set up with more than one battery YOU SHOULD NOT USE THE SAME TYPE OF BATTERY IN BOTH CIRCUITS!!! You should use a "Starting Battery" in one and a "Deep Cycle" battery (or batteries) in the other. They are VERY DIFFERENT. The "starting" type is designed to give out, in simple terms, a big burst of power for a short time - such as is needeed to start the engine. That's why they are rated as having a high number for "Cranking Amps", and a relatively low number for amp. hours. It is NOT designed to be deeply discharged and then recharged over and over. This will cause the plates to deteriorate very quickly and premature failure will result.
The second curcuit should be used as a "house" circuit, and should be used to power everything else on the boat. Here a "Deep Cycle" battery should be used. They are designed in a very different structural way and are designed to give out a smaller flow of power over a long time. Most do not even have a "Cranking Amp" rating, becaus e that's not what they are for - but they have a relatively high amp. hour rating. They "don't mind" being deeply discharged and recharged over and over ... that's what they are built for ... but they do NOT like to have to put out a big burst of power.
It's simple, really - use a "Starting Battery" for starting and a "DeepCycle" battery to power everything else! Hence the multi-position switch. Set the switch to "1", the Starting Battery, and start the engine. Then switch to "Both" while the engine is running to ensure that both are fully charged. (Note - if you have the proper type of batteries set up DO NOT start the engine in with the switch in "All". Doing so will "ask" that Deep Cycle battery to do something it is not designed for.) After you shut down the engine, move the switch to "2" and the Deep Cycle battery(s) will be the only one(s) connected and will power your accessories. When it's time to re-start the engine, move the switch back to "1", and repeat the above.
In this way you will be using each type of battery as it was intended and you will not only gain optimal performance from both battery banks, you will also get MUCH more servicable life from your battery investment.
BTW - for those of you with only one battery, you should be using a "Dual Purpose" type battery. It won't have quite the cranking amperage of a true "starting" battery, but it will do the job perfectly well, and it will tolerate many more discharge/charge cycles before it goes bad than would a "Starting" battery.
"Automotive" batteries are all "Starting" types in their construction and are not intended for use in boats where they will be asked to deliver power over long periods. This is borne out ny noting that if you even leave the dome light on in your car overnight it will kill the battery!
Uh - in case you hadn't noticed, using your electrical system properly - by which I mean: as it was designed to be used - requires moving that fearful switch while the engine is running!!! That's what it was designed to do, and as long as you don't accidentally turn it to "Off" while the engine is running everything will be just fine.
On La Nostra I have a 950 cold cranking amp starting battery to turn over the big 82 HP Perkins. Once fired up I switch to "All". After I shut the engine down (either at the end of the day or when sailing) I switch to "2" and run off the four 6-volt Deep Cycle Golf Cart batteries - two in parallel, then in series to get the 12 volts for the system - and run everything from the approximately 600 Amp Hour house bank.
I've run things like this on all my boats. I typically get 4 or 5 years from a set of batteries. The ONLY time I start on "All" is if for some reason the starting battery won't kick the diesel over - which is extremely rare.
I should also add that I never plug in to shore power - we do not have it available anywhere I sail. Instead I use a KISS wind generator and two 80 watt solar panels and am able to run the fridge, freezer, water pumps, lights, radios, etc. for days on end without starting the engine.
Hope that puts people's minds at ease - and will also save some of you from spending big bucks on the wrong kind of batteries to do the various things on your boats.