If battery 1 is selected, battery 1 will receive the charge. If battery 2 is selected, battery 2 will receive the charge. If all/both is selected, both with receive the charge. You won't see any performance gains by using it on both/all and if you let them run too low with it set to both/all, you've defeated the purpose of having a second battery when you can't start the boat. Personally, I run battery 1 one day/outing and then battery 2 the next to keep both charged and ready to go if one of them were to fail.
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