Some people also take the plastic "rail" off that goes on top of where the front doors rubber weather stripping is, and run the wires down the strip and run it through the open door, but some people get leaks that way.

....Not sure how you would get leaks that way if done right... ...Mine runs down the right side and then under the wiper cowl and across to the battery area....

Not sure how you would get leaks that way if done right, mines been that way for over a year now and never leaked, nice clean install and no drilling.
Mine runs down the right side and then under the wiper cowl and across to the battery area

If it were my Jeep and I didn't want to go all ghetto, I'd remove a rail drill into the roof under a mounting foot (drop the headliner first), drill into the foot so the holes line up, re-mount the rail, drill into the plastic mounting bolt cover on the rail and rout the wires. If you drill only as big and to need and use snap grommets and silicone to seal the holes after the wire is routed, you should have no leaks since there's no direct path into the cab.