I have been laboring over the charging system in my boat as I know the alternator is only outputting 13.6 volts. I have a spare 130A alternator to put in that is internally regulated. The charging on the boat is configured like this:
4 battery banks
Start Bank: 2 4D Lead Acid (Wet Cell Batteries)
House Bank: 4 8D AGM batteries
Bow Thruster/Windlass: 1 8D AGM battery
Gen Start Battery: 1 Group 31 Lead Acid
The house bank is charged by the alternator (130 Amp internally regulated) or by a Xantrex inverter/charger.
The start bank is charged by an echo charger off the DC Bus that handles the house that is charging from either sources.
The Bow thruster Windlass is charged by a battery isolator that connects to the house bank DC bus. It also allows paralleling of the house bank and bow thruster battery.
The generator battery is only charged by the alternator on the generator.
With mixed battery types this setup allows each bank to be charged independently but with no alternator charge controller for the main house bank or any of the other banks. The Xantrex charger is set to charge AGM batteries.
I don't see anything wrong with the basic setup, other than the low voltage output of the existing alternator. I am concerned about the controlling the alternator charge on the AGM house bank and not having some means to charge the generator start battery when on shore power. I think I can solve the later pretty easily; however, with an internally regulated alternator, I think I would like to get a little better handle on controlling the charge thrown into the house bank to prolong the life of the AGM batteries. I have Link 2000 monitor on the house bank as well as a Balmar Smart Gauge looking at it so I can monitor the SOC pretty well. I see two routes, first going with a new Balmar alternator and external voltage regulator or a Sterling Power alternator to battery charger. I had a Balmar alternator and MC-614 on a different boat and other than "lunching" the first alternator on engine start, it worked fine for 3 years. In this situation, I am favoring the Sterling Power product as it uses my existing alternator(s) and doesn't require much in the way of modification in the engine room.