None of the boxes are that big. I have a 96 Acura Integra, and there's tons of room on the right and left trunk panels. Everything is hidden behind the carpeted stock panels. Trucks like yours usually have tons of extra room behind the dash where you can mount things like Ipod adapters, bluetooth, etc. The rear wall of the cab behind the back seat is a great place to mount stuff. I used to carpet a piece of 3/8 plywood and mount all kinds of amps and signal processors in Ford trucks.
The hardest part of my install was getting the stupid head unit to go in the hole. It's so tight behind mine that I had to thread each wire through individually to get the clearance to push the unit all the way back.
If you're going exotic and installing new speakers, amps, tv tuner, XM, etc., $985 actually doesn't sound too bad. I'm not sure I would do it for $985. LOL I installed a really exotic Kenwood nav system in a Lincoln Navigator belonging to a friend of mine with multiple flip down screens, Xbox, tuner, amps, XM, etc., and it took me over 50 hours. That might give you some idea how much time some of this stuff takes.