Maybe a stupid question but I have never messed with a 24v system. I have a 2 batteries wired together for a 24 volt trolling motor. My question is can I wire a 12 volt winch to just one battery or is an isolator needed to wire the winch?

You can wire a 12 V switch to just one battery but while wiring in a series for the 24V I would be very careful about running something 12V off of just one of the batteries. Thats not good for the batteries wired in series. Draining one of the two batteries in series will put strain on the other battery.

I have my running lights hooked up to my 12V battery however when I am in series like that I have a DLS-27-40 convertor running off a generator keeping them charged up so the batteries never go below 12 volts or so...

This is for my bowfishing set-up