The onboards will boil too(the Tech has changed a bunch since i last checked so they are better now). Just dont leave them on for a long time and your set. When i come back from fishin i plug in then unplug the next morning.
i use a 3 bank(2 troll, 1 engine) cause the livewell, aerators, and stuff use the engine batt and are always drained too because the engine doesnt run long enough to charge it.
I would post in the tournament section of LSCN.net and see what everyone is using. What kinda of boat do you have. If you put the charger in the boat dont mount it flat. I was told by many that the boats flex enough to hurt the circuit boards if you flat mount them. Everyone said to stand them up on their side if your using a bigger 2/3 bank