Running wires to power lights on your rack is all very easy except perhaps getting it from the window to the roof rack. Here is what I did:
Run wire up the channel in the windshield weather stripping. If you get the right size, it fits in nicely and stays put with nothing else required. I have three sets of lights I power with two wires, one on each side.
The wire also fits perfectly through the plastic piece at the base of the window.
WRT firewall, there is a nice plug you remove, punch a hole in, and turn into a grommet. Run the wire through that and the wire drops down near the fuse box, so you can hook the power up to a relay or switch pros or whatever in the engine bay, and run a wire to a switch in the interior. I have a switch pro running through there, but I have a few other power wires running through too.
I don't know how easy it is to hide wires under the weather-stripping up top.
Maybe that's the excuse you need to buy an aftermarket rack :-)