Which smart RELAY are you using... I am planning on using the BLUE SEA SIACR model here for charging additional battery bank at the same time the alternator is charging the truck start battery. When not in charge mode then the additional batteries are switched out of the truck start battery circuit. This keeps you from ever running down your truck start battery by accident.
I would imagine the controlling factor is going to be the truck start battery since it is very close proximately to the alternator.
This is the basic concept for my planned setup
(Disregard the boat motor-this will be my truck alternator system)
I'm hoping this is going to work for me. I will be charging additional deep cycle flooded cell batteries.
Roy Ken