Yes, you want to have the charge controller leads attached to both batteries. The absolute ideal situation is to set up a distribution panel that can charge all batteries equally and will discharge them equally. You may already have one but they can sometimes be obscured in the pile of wires.
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John
2016 Thor Hurricane 35C with pups Piper and Annabelle
2013 Ford Fiesta toad
FMCA - F457085
Blog - https://traversity.us
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