I JUST got my truck back an hour ago.
Yes, the quick disconnect does disconnect both the positive and negative wires, thus taking the second battery completely off the truck's grid when disconnected To me, that is a safety feature.
My second battery was a side post battery, so I connected the cables to it accordingly.
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I connected the positive cable of the second battery to the same post on the master fuse block on the passenger side firewall (before the fuse) as the positive cable from the primary battery.
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I connected the second battery to the same stud on the block just ahead of the passenger side valve cover as the primary battery.
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The quick disconnect is located near the driver side firewall, just under the brace by the hood hinge. The cables going from the second battery to the quick disconnect are laying between the main fuse box and the inside of the engine bay next to the front left quarterpanel.
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