a battery isolator only isolates 1 battery from another when the vehicle is off. When it is running the isolator is 'open' both ways. When the vehicle is off, the isolator prevents your system battery from using your vehicle battery for power. This way you can run your system battery down to dead, then start the car up without needing a jump. Adding an isolator doent not cause an alternator to 'see' multiple batteries, it still just sees 1 large one.