If the charger you are talking about is a shore power charger, then the ACR will defeat your attempt to use a multi-output charger for each battery. As soon as the charger is turned on, then ACR will combine the batteries and your charger will just be providing half it's output to each battery, but they will all be connected together anyway.
You want something that is the inverse of an ACR. When the charger is on, then the two batteries would be disconnected and the charger could charge each battery according to it's own need. Once a charging source goes away, the batteries would be combined again.
That's probably a bad idea, and unless you alternator has multiple outputs as well, because it wont work when you're charging with your motor.
Anyway .... if your 2 house batteries are a matched pair, same age, etc., and they're both in good shape, then charging them as a single bank should be just fine, and a lot simpler. The only time you might want to charge them independently would be if they were different types, different ages, or in different conditions (one dying, one good), but you shouldn't be using them in a single bank if that's the case.
BTW, I use an ACR between my starter and house banks. My alternator only has a single output. But, my shore power charger has multiple outputs, and I have wired it up so that when my shore power charger is on, then, via a relay, my ACR is disabled so the shore power charger can charge and maintain the two bank independently.
Chris