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One of my batterys is used for starting, other has all the auxillary stuff hooked up to it. When theres a small current draw when the car is turned off, it will kill both batterys and i cant start. A isolator can seperate the two batterys when the ignition is off, so it always keeps one battery available for starting (ie. if my auxillary battery dies, main one will still be charged/ready because its not connected to the auxillary). I've heard battery seperators do the same thing....? Which is better/

 
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I've never heard of a battery seperator before. We always use battery isolators when installing a second battery if they want it set up that way. Otherwise, if we're doing an alternator upgrade as well, we usually just run the batteries in parallel off the alternator.. well, obviously not the ground wires but hey.. there's enough smart @$$es on the forums that I don't want anyone to take it that way. haha Anyway, I recommend Stinger. You should be able to get it at any car audio shop.. otherwise, you can order off cardomain.com

 
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There's the diode kind and the relay kind, relay kind is probably what you want.

 
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yes get a relay operated battery isolator. never heard of a seperator. isolator is probably a lot more safer.