I have the wiring ran to the cargo area then to the lights through the rear passenger side roof rack mounting foot. I drilled a hole through the mount that is covered by the oem rack foot cover, after running the wire I filled the hole with sealant to keep water out of the cab. I also had to make a small notch in the foot cover so the wire get through one of the openings in it. You can't see the hole that actually goes into the cab but if you're really looking (and standing on the rear tire or rear bumper) you can see the notch on the inside of the foot.
You can see the wires right now because I just put the new sport rack on and haven't gotten larger wire loom to cover the quick connects I put in. It looks better without the quick connects and only the smaller loom but I think keeping the disconnects in there is a good idea.
If you search on here, there are also ways to do it without drilling, but the wiring will be visible in some areas.
p.s.
ROLL TIDE