I would just hook it up via isolator and run your accessories off of it. The isolator only allows the battery to be re-charged and does no allow current to flow the other way, basically it will not have any effect on your starting system.
Another option would be to run a heavy duty solenoid that activates when the truck is running via oil pressure switch or something similar to keep the battery charged, then wire a momentary switch inside the cab just in case you need a little extra boost for starting.
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