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Yes, it treats them as separate batteries, with leads going to the batteries independently. I mounted this up onto the door near the dead crank switch (and moved the wiring diagram to the 'front' of the machine, to the side of the fuel tank. I cut in a bulkhead wire entry port. If you want I will find the thread on it where I show my installation. All you have to do is unplug this charger before running the machine, and otherwise it just optimizes the batteries while its in standby.