IWF if your charger is like mine it is a 2 bank hooked to cranking on one leg and the other leg is hooked to 2 12's like you are talking about. It senses the amount of charge on each bank. If in most cases the cranking battery needs little if any charge the extra is then routed to the one needing charge. So if your charger is a dual 6 it would put 6 to each bank until the cranking battery is charged then it would shift part of the amps from cranking side to trolling side when cranking is fully charged all the amps for both banks would be directed to trolling batteries. With my Terrova I have never had a problem recharging overnight. My charger is a ProMariner 6/6