A bit confused here. Are you saying the winch should be wired to both batteries? There are lots of us with dual batteries that only wire the winch to one battery. In my case I have the option of bridging the batteries to winch or jump, etc but I know of a lot of people that only wire to one battery.
If your batteries are connected in series as opposed to parallel I don't think it matters much either.
Please correct me if I misunderstood.
-Sam