I had the same thoughts as you did about the ipod cable and usb cable. I decided to put both in the upper glove box. I ran them both through the hole in the upper left corner (some sort of sensor thing is there already). There was plenty of space and I didn't have to modify/cut anything on the truck.
I went with the glove box since I want to keep my ipod out of sight for when I park downtown. That 7' cable really goes a long way though!