If you are wondering if the charger is charging both, when you come into the dock next time, can you park the boat and before you hook up the shore power cable with the switch in the off position use a multimeter to measure the voltage of each battery? Then hook up the shore power cable, verify at the distribution panel that there is power to the battery charger, and with the switch still off, then use the multimeter to test what the voltage is at each battery? I believe that in the second test each battery will read about 14.3-14.6 V (the voltage that charger is putting out) and in the first test before connecting the shore power line to provide a/c current to the battery charger to run d/c current to each battery that each battery should say about 12.2 to 12.6 V. I think if you run a test as I described you see if the voltage downstream of the switch is proving that the charger charges both batteries when in the ON position. Does that help?