I just went through all of this for my '99. There's some good info at etrailer.com; specifically, have a look at:
http://www.etrailer.com/faq-cbc.aspx
If the link doesn't work, go to the brake controllers page, go to the commonly asked questions link at the top, the go to the installation guide at the bottom of that page.
For my truck, I had to connect the wires at the power box under the hood, and run a pair of wires back for the trailer brakes and the aux 12volt in the plug. The other wires for the lights are all in the back harness near the spare tire.
Installing the controller under the dash was probably the easiest part; running the wires back and hooking up the connector plug was a bit more effort, but in all, I'd say it took a couple of hours.