Point is you can do it any way you want.
You will not hurt the altenator charging both batteries. I do it all the time.
Sometimes I run all day with the switch in the 1 or 2 position only, then next time I change to the other battery, next time in the both positon.
Again either way you won't hurt anything.
I also have an onboard hard wired trickle charger which I use if I won't be on the boat for a while. Still I've never had a problem with charging any of these 3 different ways.
Good Luck.
V.
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