I saw on another board (or it may have been this one, it was a couple years ago) how to do mine. Take the plate off under your windshield wipers. Pop the wipers off, and take out the screws. Pop the hood and there are a few more hidden under the gasket where it meets the hood. I laid my wires in there stuck them through the water drain in the middle. You'll see what I'm talking about when you take the cowl off and into the engine compartment, through the big rubber grommet at the fire wall near the master cylinder to go inside.
That's where the wires enter into the cowl.
Bad pic but thats the grommet I ran the wires into the cab.
Nice clean look IMHO.
(edit: just saw this was in the YJ forum sorry. Don't know if you can do that)