Their main HQ is in Spring, though you can go to any town that is under rebel control like the hub and go to the small building with their flag, usually it's a recruitment center. You can talk to the person behind the counter and ask to join the rebellion. The same thing goes for joining the empire. Finding a recruitment building in the towns/cities and talking to the person behind the counter.

Rebels have not many cities under control. Spring, Hub, Drin.