The ACR would charge both batteries regardless of which position you have your switch in. In off, on, or both. the batteries would be charged by the charger/alternator.
I assume you have no battery separation on your loads. All your electrical loads are serviced by the battery selected by your switch 1 or 2 or both. I also assume your alternator will only charge the battery selected in position 1 or 2, not both. In both; both batteries would be charged.
The system I was looking at will allow separate loads on two different batteries with one common charging source.
My goal is to shed all load off my a battery except for starting the outboards and use the alternator/onboard charger to charge both batteries. This way i ensure no dead battery when I fish all day not running my outboards much. This happen more than I care for it too happen. This system I would do this if it works as advertised without any manual switching on my part.
It is on order; I will let you know if it I like it or not.