I run the positive cable from the second battery straight to the isolator and from the isolator to the winch, i have my second battery connected and charging all of the time as i have other things running for it.

I would go for an isolator rated higher than 300 amp continous use. My winch pulls up to 390 amps (thats what the instructions say). Your winch works really hard when your axle deep in muck and trying to pull your self up and out.

DONT FORGET TO GET A WINCH BLANKET, BE SAFE