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depending on what type of isolator you are talking about , an alternater does not have the complexity to charge two batteries at the same time it will always charge the lowest battery and that one only , you can install a manual changover having the batts separatly wired or there is a product on the market in new zealand that uses a diode to pick up the peak voltage and switch batts prob is i dunno that name of this device , if you are clued up with the net and diodes and soldering you could knock one up yourself.
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Wassup Manus
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