Salmonseeker,
I have the same setup as you. I use automotive style cables, 4 gauge to make all of the connections. I used an anti-corrosion paint on all of the of connections.
I took the negative from my motor and hooked it to the negative on battery #1. I also hooked my accessory ground to the negative on battery #1. I then ran a 4 gauge "jumper" from battery #1 negative to battery #2 negative.
I took the positive from the engine and hooked it up to the "common" lug on the switch. I also hooked my accessory positive to the "common" lug on the switch. I then ran a 4 gauge "jumper" from battery #1 positive to the #1 lug on the switch. I ran another 4 gauge "jumper" from battery #2 positive to lug #2 on the switch.
The way I use this is simple. Each time I go out I alternate my battery selection. I very seldom run it in the "both" setting. I have always heard that this works best for the batteries and the engine's charging system.
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