Mike,
Now you have me a bit confused (beyond my normal confusion, of course). You say that "an alternator is not a charger...it's a 'maintainer'." I have always been under the impression that an alternator recharges your battery as the engine runs. If I have a dead battery in my car, for instance, I can usually (if the battery is fairly new and in good condition) jump start the car and let it run for a while. That has always recharged the battery (from the alternator, I assume, since there is nothing else on the car that would recharge the battery). Is a marine alternator different?
If I run down my boat's house battery over a weekend on the hook, won't running the engines recharge the battery? I've done this (before buying a Honda EU2000i generator) and it has recharged my house battery, I believe. Once I've started my engines on my starting battery (Position 1 on my battery selector switches), I've always switched the battery selector switches to all and have never had a problem with the batteries. When I'm hanging on hook, I always have my battery selector switches on my house battery (Position 2 on the switches).
I'm just trying to understand why an alternator doesn't charge, only maintains, the batteries.