OK I have been thinking about this for a couple days now and it sounds like it will work (at least it does to me) but I am not 100% sure.

I have 2 batteries and a 2 bank charger that I just put in. I want to run it like this:

battery #1 - motor and whatever is on the boat electric panel (the alt in the boat should charge it enough to keep up with the boat itself)
battery #2 - amps, power inverter, leds, and everything else

Would I have to put one of those switches on the system and change things around or run it like I am thinking? The reason I ask is, on a bass boat you have 2 batteries that run the boat off of 1 and the trolling motor off of 1 then charge it when you get home.