Something I've observed with charge controllers is they're rated in amps OUTPUT to the batteries. A 60 amp controller would give you 720 watts at 12v, but 1440 watts at 24v, for the same price. So it might make sense to reconfigure the batteries to 24 or even 48 volts. The whole system would be more efficient. BUT Yeah I know this brings up a whole host of problems...
Inverter... You'd probably have to upgrade to a 24v or 48v inverter. No small change but if you're thinking of upgrading anyway...
How to run all those 12v gizmos (not to mention the engine): That would require a smaller battery bank configured to 12v, maybe a single 8D or a couple golf batteries. Charge 'em with another MPPT controller off the main battery bank. WHEN I get around to upgrading my system this is probably what I'll do:
My "proposed" system (for MY boat): Probably 8-240w panels for about 2kw configured for 48-100v. A 48v, 60 amp MPPT charge controller (2880w, capacity for up to 4 more panels). 8 golf batteries in series for 48v (I like golf batteries). A 48v, 3000w inverter/charger for AC (with any luck it'll run the airconditioner, too). For 12v service I'd have two more golf batteries or an 8D for 12v service and emergency starting, charged off the main 48v bank with another MPPT controller (yes you can use an mppt controller to step down a higher voltage).
Anyway that's the "plan". Once the current battery bank croaks I'll get serious about it.
Will it work for you? I have no idea.