I am far from the expert on battery charging, but...

When I installed solar charging I went for a two-battery setup (with priority). 
The AGM batteries really like to be fully charged and, usually, we don't 
provide them with enough charging (unless you have shore power and charge them 
at the dock). The alternator does a great job up to about 80% of the battery 
capacity and after that you would have to run the motor for a long time to 
reach full. This is where a decent solar charging controller helps (it provides 
the float for days on end (when you are not sailing)). 

I would connect your solar charging to the AGM batteries (the house bank). 

I have a somewhat different setup with all batteries AGM, but I don't split 
them into house and start, but rather, into main and spare. So I start the 
motor and run the lights from the same battery (I don't have refrigeration, so 
I cannot say I have much of a house load). This way, the alternator charges the 
battery as much as it can do in the short periods of motoring, but the solar 
charger continues and completes the charging when the boat Is not in use. The 
solar controller  fills the main battery first (90% preference) and when it is 
done, charges the spare battery. So far it works fine (both batteries full when 
I arrive at the boat). I cannot comment on long-term effects, as I have this 
set-up since the beginning of this season. But it works.

my $0.02 (CAD)

Marek 
in Ottawa
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