I'm in the middle of updating my web page, but I'll share these photos for the time being.
Once you have decided where you want the wires to come through, remove the roof rack. I did not want the wire coming from the front of the truck so I decided to use the middle foot of the stock roof rack. Under the foot you'll notice 2 nuts, there is no reason to remove these(unless you're married then it's already taken care of). I drilled in between the two and ran the wire from the inside out.
With the foot off the roof rack align the wire and mark an area to drill.
Use silicone and black rubber sealant along with rubber grommets to protect the wires and seal the hole.
Here it is before I added the finishing touches.
I'll have a more detailed how to once I finish the page. At least this gives you an idea.