You don't indicate which boat you have, or engines, so don't know if this will work for you.
1. Two (2) starting batteries. Each one wired through the usual Off-1-Both-2 battery switch. Starboard engine connected to terminal "1" on both switches and port engine to terminal "2" on both switches. Either or both batteries can be used to start an engine, but the NORMAL line up is with one switch in position 1 and the other in position 2. Each engine starts on one battery and charges that battery.
2. One (1) or (preferably) two (2) batteries in parallel as the "house bank". This bank is connected to an "On-Off" battery selector switch. The Auxiliary Charging Lead from both engines is connected to the battery terminal on the switch, so either - or both - engines charge this bank.
3. If you have a 3-bank charger, as we do, then you can connect to each of the starting batteries and the house bank.
We repowered from a single to twins in Oct 2005 and I set up this arrangement. I just replaced all four batteries this summer - only because it seemed prudent, not because they were exhibiting problems. We are in the water all year, and use the boat all year.
I can send you photos if needed.
Brian