You won't harm the electrical system with such devices, assuming of course that they're properly specified and installed. Do be aware that many are not really designed to switch under load, so turn off electrical stuff before operating the battery disconnect. Also, if your isolator is not actually isolating, putting the cutoff in for one battery will make the other battery drain more quickly from the various parasitic loads.
Incidentally, it may be easier to connect it into the negative lead rather than the positive lead; the effect is identical in either case. An open circuit is open no matter where it is disconnected.
If only one of the batteries is getting discharged, that's pretty conclusive evidence that the two are indeed isolated somehow or another.
