You can use a 3 bank system, but I don't think it is necessary to charge your starting battery since your alternator takes care of that battery. I'm running 3 batteries (one starter, and two accessory batteries) and only use a two bank charging system for the accessory batteries. Just to let you know, in the 3 or 4 years of using a 2 bank charging system I haven't had any issues with my starting battery.
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