Haven't done this, but:
* how many controllable sets do you want, i.e. how many switches are you using to control them? The fewer the better, more means more wires you have to seal.
* how much current / how many watts total load?
I would wire all the fronts on one circuit and all the rears on another. Run the wires out of the cabin via the holes behind the rear tail lights, then stuff them under the outer edge of the weather stripping for the rear hatch up to the top and out onto the rack between the hatch and the roof. The ground wire can go the same way, except just stuff the ring terminal under the first bolt you come to instead of going inside with it, if you have a late model (97+) you can use one of the hatch hinge mounting bolts.
Lots of lights is one of those things everyone wants to do when they get the idea, but then you realize they are easy to break and you don't use em much. Forget I ever said this if you do prerunning/jeepspeed...