Peteramc,
I agree with Comraderie that your system needs redesign and replacement of at least some of its components. Mixing battery types, voltages, and ages in the same bank is never a good idea. The fact that the 6V batts are distorting is a sign they're shot -- get rid of them before they start leaking.
It sounds like your 12V - 6V melange was intended as a house bank (lights,
pumps, etc.) If so, you can replace it with either 12V or 6V batteries (with the 6V batts wired in series for 12 V output), but don't mix the voltages. House banks should be "deep cycle" batteries. If this is the bank you use primarily for starting the engine, then you can probably get by with a single 12V starter battery (some companies make a combo "starter-deep cycle" which is also an option).
A hint on buying replacement batteries -- don't buy them in a marine store. One advantage of wet cell (lead-acid) batteries is that they have wide industrial uses, golf carts and fork lifts being examples. Industrial users won't put up with the mark-ups we normally suffer at marina's boat store. Once you've redesigned the system and determined what you need, buy the batteries from an industrial supplier where the prices should be substantially less than the local West Marine (last time I bought batteries the price difference was over 30%).
You'll find that replacing batteries is a major investment. Read up on the topic -- although somewhat intimidating for those without an engineering degree, it's not rocket science. The keys to a good return on the investment are fairly simple: design the system properly, buy good batteries (Trojan offers very good value for money), and then take care of them. If you keep them clean, watered and fully charged when not in use, quality deep cycle batteries will last a long time. (Mine are 6 years old and may have another year or two in them).
You mentioned that you have two battery banks. While I agree with Comraderie that it's better to have one starter battery and one house battery bank, space considerations may make it impossible to physically put all the batteries together in the same bank. If the groups of batteries are not too far apart, they can be wired into a single bank, which is probably the best solution. If they are more than a few feet apart you may have to have separate banks. The problem in having separate banks (and for that matter mixing types, voltages and ages of batteries) is in how they accept a charge and how the voltage in the batteries registers with the voltage regualtor in the charging system (either the alternator or AC
battery charger). Trying to charge two banks from a single charging source (or charging a mixed bag of batteries in a single bank) means that some of the batteries will probably get less than they need and remain chronically undercharged. This reduces both their utility and useful life.
Last point, I'd recommend you hire a marine electrician to help you with the installation of the new batteries. (You might also hire an electrician to help you with the redesign, or at least to check what you plan to do). While 12 V batteries won't kill you, they need to be treated with great respect. Getting the wiring wrong can be dangerous and might damage the batteries / chargers, etc. Unless you're supremely confident that you know what you're doing, fork over the $60-80 per hour you'll need to hire a good electrician.
Battery Replacment advice
