Funny this question came up
 

I've always run with both batteries on. I've also always had trouble with the #2 battery. This year it was dead again. I got to snooping around and found my battery switch was wired wrong from Baja. In essence the #2 battery did nothing but sit there and go dead. It only took me 5 years to discover that

Start and run on 1. Raft on the other. Both off when racked.

There was an article in Hot Boat (I think) about just this subject. It said to use a Marine "start" battery for engine starting (perhaps bat1) and then a "deep cycle" (bat2) to power radios, a/c, fridge, etc. The problem they came up with is different charging demands voltage wise, and an alternator that didn't know the difference. Then they recommended some advertisers product for charging at different rates, etc.
No, I'm not sure what all this really means, I just do like craig223 does.
:D :D

When I purchased my boat the man who owned the dealership told me to start and run on battery #1 one time, then the next time out use battery #2...He told meto do this so if there ever was a short or some sort of drain I would not drain both batteries at once...so this is how I have run for three seasons now...knock on wood no problem so far.

I also read the article in Hot Boat mag. I purchased my boat used last year and someone put in 2 deep cycle batteries. I just replaced the weaker one with a marine starting battery(battery 1) and kept battery 2 as the deep cycle. I will start and run on battery 1 and switch to battery 2 for raft-ups, etc.

The article says not to let the alternator charge-up a deep cycle battery because it charges it too fast. My Interstate battery rep agrees. Plus my starting battery has more MCA(marine cranking amps) 1000 amps. I'll charge my deep cycle batt. with my shorepower charger.

Hopefully this will let my batteries "live" longer.

Toolman