"My truck is lowered quite a bit (5.5 in the front, 7 in the rear). "
With that radical drop if you have full length headers they will be hitting everything ! Speed bumps, driveways, manhole covers, you name it !
Consider going to shorties. The truth be told, there is little, if any benifit to full length as their performance gains are seen at the top end of the RPM range. A good set of shorties, from Sanderson for example, will actually out perform full length headers in the RPM ranges we live in most times, the 1,500 to 3,500 range.
Here is a HP / torque chart that illustrates.
http://www.sandersonheaders.com/images/shortvslongtubechart.gif
A good muffler shop can tuck the rest of the system up above the bottom of the frame rails. Either inside or out. If you run them inside the frame, you still need to deal with running the tubes either under ot through the rear crossmember that supports the trailing arms. If you have a tank under the bed, you will need to figure a way to keep the exhaust inside the frame rails and around the tank.
On a panel or fleetside the path of least resistance is outside the frame rails tucked up behind the lower rocker panels.
The only visible portion of my exhaust are the dump tubes inside the fenderwells, and the chrome down turns at the rear corners.
DV