In simple terms, I've connected the MPPT
output more or less directly to the house (main) bank and not worried about the second battery. All the guff that uses power with the 1-2-both-off switch in the "off" position (sound system memory, bilge
pumps, USB chargers, "that" light that needs to be switched on first of a night etc) runs off the same bank. The other battery just sits there and does nothing with the boat powered down.
To complicate just a little bit, I have a Victron battery monitor
so connect the -ve output of MPPT to the opposite side of the shunt to the battery so the charge can be monitored. I also use one of those auto resetting circuit breakers used for car driving lights between the battery and MPPT controller +ve lead "just in case".