Some battery chargers are designed to handle multiple banks. For instance, the Xantrex Freedom 20 inverter/charger has two "echo" charger connection points, and can charge THREE banks without any trouble.
Absolutely, and we'll be setting up our Freedom 30 to "echo" the engine start and the thruster battery. That's got limited usefulness to us, however, because we're not likely to have the genset, and thus the battery charger, running when we're using the thruster while maneuvering around docks and such. So, I really would like the have the thruster battery getting a charge from the engine alternator, as the engine will be running when the thruster is in use.
After doing some research and going round and round, I actually think Beneteau may have set it up in a reasonable manner (who'd a thunk it!) with the thruster battery connected to the house bank, but via an isolater so that it gets charge from whatever is charging the house bank, but it doesn't draw off of the house bank), so I think we're going to leave it for a while and see how it goes. If it turns out I don't like it, I think I'm just going to remove the thruster battery, get oversized cables and run the thruster off of the house bank. That way, I essentially have a two bank setup which is very easy to isolate and charge (leaving aside the genset start battery, which is going to live in its own universe).