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Assuming you have switching for your batteries so they are not all combined at the same time all the time, with an isolated starter bank for each motor.
If you have an isolated starter battery for each motor as I do (actually two in a pair for each motor) and a house bank for inverter use, then that would be three banks of charging.
If you have just a single battery for each motor, that's a two bank system, but you might go ahead and get a three bank charger in the event you want to keep a spare battery hot or use it for inverter use.
The chargers will come with directions, should be a piece of cake. I will confirm again, May of 2009, the system I installed remains to be TOTALLY TROUBLE FREE and one of the smartest things I ever did to the boat. Prior to installing this unit, I was cooking batteries on a regular cycle. Works great.