What year is your truck? I know on the older body style (82-93) there are grommets in the firewall just behind the brake pedal with wire run through them; that's where I have my power wire run. I'm not sure about the newer body style. After it comes through the firewall, it runs under the driver's side door trim, which comes off with a screwdriver. From there it runs into the back seat.
One word of advice for running through the engine compartment: ZIP TIES! These things rule. It's not a good thing to slice through a dangling power wire with your fan (trust me!)