T&T: Advice charging inverter bank from alternator

[Steve Sipe]

I'm puzzling over the best way to handle my battery charging without 
reinventing the entire system, but the more I focus on it, the more I am 
thinking I may need to re-evaluate. The PO added/changed some things 
without (IMO) regard for the larger picture. Briefly as I can, battery 
inventory is

8D start
4D gen
(2) 8D house
(4) GC AGM- 3kw Freedom inverter
(2) GC wet- on boat deck for boom winch
AGM -24V thruster

Charging is accomplished by:

Alternator (stock 150A? on Cummins 5.9BTD) does house & start -via an 
isolator.
Inverter bank stands alone, charge via inverter only (genset or shore 
power req'd)
Boat deck by portable 15A manually (ditto genset or shore power)
A phase III charger does house, gen, start (ditto power)
thruster via dedicated charger (ditto power)

Not what you'd call integrated systems. It works OK, but

I'd like to be able to charge the inverter while underway, but the 
inverter bank is AGM, the rest are wet.
I'd like not to have to drag out the portable charger for the boat deck 
bank.
I considered an echo charger or a current limiting battery link for the 
boat deck bank, makes sense to charge it from the engine. (Cabling is 
not easily accessible)
I'd prefer to eliminate the isolator in favor of a combiner, although 
charging the house bank is not a problem.
I'd like to end up with a smart charging regulator for the alternator, 
but the differing battery types are a problem. (I am adding ventilation 
for the alternator & E/R.)

Any suggestions on how to progress to a more integrated system while 
accomplishing some of my objectives on the way, and not backtrack? Or 
should I start over? <G> Our long-term objective will entail more 
anchoring and cruising than marina stays by at least 4:1.

Steve Sipe
Solo 4303 "Maerin"
Upper Chesapeake (on hard)