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You need both batteries to run the glow plugs and starter. Diesels need to spin over fast, and are harder to turn over than a similar sized gasser because they have a much higher compression ratio.
Unless, of course, he is planning to add a third battery for other reasons.
I can't imagine an isolator kit not coming with fairly complete instructions. If you are so inclined, pick one up at a parts store and look at the instructions before you do any work. If you don't like the looks of the description, take it back. But do NOT isolate the second factory battery or your truck won't start.