How does an isolator work?

ive been told it isolates the batteries so that only 1 battery is used at a time to prevent fast wear and tare on the batteries from charging off of eachother ETC... i've been told it allows only 1 to work... but the way my stuff is set up just throws the ol wrench into the gears.. you know...? how can it isolate the battery and allow only one to be used when the car is off so i can still start my car... if my amp is wired to my aux battery directly... and my lights inside the car are hooked up to the front along with the ignition to start the car... does it supply the battery from the most charged battery when say the front battery is dead since they are still linked via posotive terminals? i'm somewhat baffled as to how it works...