[jclark003]

Are you sure you have three separate battery banks? I've seen some installations that have a start bank that services both engines along with a house bank. One engine alternator charges the house and the other charges the start. That could explain why you have only two charge wires. Alternatively with your setup one wire could go to the house battery, the other going to an isolator that feeds two independent start batteries. This may have been done because the previous charger only supported two bank charging.

Regardless it would seem to make sense with a three bank charger to wire direct to batteries (assuming you do have three separate banks), leaving the isolator in place for the alternator to charge two independent batteries.

If unsure follow Uhehner's advice and get a marine electrician to give you a hand. There are a lot of different ways to wire in charging systems.