With one of the modern charger/maintainers, you can leave them plugged in all the time.
Personally, I prefer to wire my ACR off the "output" side of the Blue Sea switch, so it is only able to bridge the batteries when the switch is "on", and then run my 2 bank Marinco charger off the battery posts (well actually, the Blue Sea battery terminal fuse blocks). The Marinco charger is a "smart" charger, which can vary it's charging output to each battery individually. Perhaps a non-issue, but I worry about having an ACR connecting the two batteries and interfering with the function of the charger.
Would be interested in hearing DevMah's thoughts on this.