Jim, I think we have the same boat. Mine is configured as such: 4 batteries. 2 port, 2 starboard. The starboard batteries are under the seat, the port are in the engine compartment. The far starboard is for the genny, the near starboard is for the starboard engine. The 2 port batteries are wired in parallel, and are shared for the house and the port engine.
I have the divi-charge battery isolator (that gold brick with the cooling fins) just to the right of the batter charger. There is also a selenoid just above the divi charge isolator that is activated by the emergency start switch on the dash (that would allow you to jump one engine from the other).
I had the Promariner 30 Amp 3-bank charger. I had constant problems with the port batteries. The tech at Promariner said I was cooking my port batteries because the charger wasn't intelligent. I replaced it with a Promariner 1230i Plus. I just did it this weekend.
The tech at Promariner offered to sell me the 1230i Plus for $350. When I told him I got an internet price for $299, he countered with $250. That's the best deal around, I think. You will have to give him the serial number off your old unit. The replacement was pretty straight forward, except I had to move the Divi Charge Isolator, and I installed the new charger sideways.
Hope this helps.