OEM Roof rack

I bought my 13' Taco used with its roof ravk so I have no idea how it goes on.
I added the XM adapter to play through the stock head unit, anf ran the wire out the back of the truck and have the antenna undrr the bed rails, as I read many people saying how good of signal they get there. I think it sucks. It cuts in and out way more than any other vehicle I have had with XM (4).
What I am wondering is are there any holes going through the roof to the headliner that I can run the wire to and have the antenna om my roof? I have read several threads of people getting the roof rack installed then having leaking problems, so there must be some form of holes.
I like to hide all wires if possible, but I need a better signal than I have now.

 

There's pre drilled holes on the rain gutter things under the weather strip

 

Are those filled by screws for the mounting of the roof rack?

 

Yes those holes are filled with the bolts that hold in the Roof Rack