Re: AGM batteries
I'd set the charger and any regulator(s) --- for the alternator, wind generator, solar panels, etc. --- to the AGM profile. The EchoCharge will take care of the flooded start battery just fine.
And, if you set it up as I suggested with all charging sources going directly to the house battery bank, with an EchoCharge or DuoCharge connected between the house bank and start battery, then there's no need for switching at all.
IMHO, it's a BAD IDEA to play with the main battery switch while the engine is running, even if it has a field disconnect circuit. Someday, you or one of your crew is going to switch to the wrong position and blow your alternator diodes.
I agree with MainSail's comments about AGMs. Been running some factory supplied numbers myself. My conclusion at this point is that there are very few boats for which AGMs make any sense at all. If you really need a battery with a low self-discharge rate which doesn't require maintenance and which can be installed on its side, then go with gelled batteries.
These have a very long cycle life, provided that you properly set up the charging voltages. Just about any modern charger or regulator has this capability.