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Battery isolators should not matter to the alternator one bit. Basically its two big, in water terms, to big check valves that only lets alternator current flow to each battery, but the two batteries cannot drain into each other. What it is is just two big diodes. The ONLY problem with an isolator is 1) fairly large and 2), because of the diode there will be about a 0.7V drop from the alternator to either battery (14.4V - 0.7V) makes about the highest value about 13.7 obtainable volts.
With the battery isolator is nice to keep say a subwoofer system separate from the the rest of the car, that way if you blast your stereo and run your one battery into the ground, the remaining one is unaffected, and can still start your car.
You can always try the big honkin' relays for 50 or 200 amps depending on your application and how you want to set it up. Relays have no voltage drop across the contacts.
I don't know on your situation, but an isolator is not required to run two batteries in a car. I have two deep cycles tied to each other with no observed problems.
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Battery Isolators???
Linear Mode
