Gawd how many boats are out there with a single DieHard battery taken out of a car?
Fastjeff, you must learn about "house"vs "start" banks of batteries. So you know, you will need at least two. One of them must be a marine deep cycle, the other can be a regular start type battery ( but I recommend a deep cycle too). You want to set up your boat in such a way that you NEVER run the start battery flat.
If you keep your boat on a trailer, you can use any old battery charger, but if you are always in the water, you'll want a good quality on board charger. There are many gazillion choices out there, so buy as much as you can afford and don't be cheap.
Same goes for the batteries. Buy Deka (east penn), or Odyssey marine deep cycle. These are the best-made ones out there and you cannot go wrong choosing either brand (made in USA).
Now here's the part where I lose people, making the proper connection between the start bank and the house bank. BTW they are called banks because you are "withdrawing" and "depositing" amperes. Anyway, you will want to keep them separate. Well, most of the time anyway but I'll get to that in a moment.
You want something called a VSR, or Voltage Sensing Relay. This goes between the charger (and alternator) and the two banks of batteries. What this does is fill up the START battery first, then when that is topped off, begins to fill the HOUSE battery. Again there are about ten million various vendors selling these, but the easiest to install and use for my money is the one by
BEP Marine. This handy little panel gets rid of your (useless) 1,2,BOTH,OFF switch, and allows for emergency parallel. Wait what's that? you ask. It's what I was referring to earlier when I said you want to keep the banks separate, until you don't.
If for some reason your start battery goes flat, dies, blows up, falls overboard...whatever, you want to be able to use the house bank to start the engine. Who wants to be fooling with undoing battery cables in a pitching sea especially if its a critical moment? Not you, for sure. So with the emergency parallel switch you bring the house battery into the start circuit and bingo off to home. You won't be surprise to learn that there are automatic switches (I have one) that will put the house bank in parallel when it senses the start bank has gone flat. If you want to get super nerdy about marine 12V systems i am your man.
Anyway I hope you sort out the electric problem. And then you'll be shopping for Balmar alternators...