Don't hook them up in series unless you have 24 volt parts!
All the factory stuff is parallel as far as i have seen. That what is simple and fewer components. It would be up to you if you use a isolator. I like to have fewer connections in high amperage circuits, so I don't have an isolator, which means that you have to use you head while using the winch. But one of the fastest ways to kill a winch motor is low voltage, so I keep an eye on volts anyway.