Under the center seat/console should be a good area.  Route the wires
underneath the carpet, and up behind the dash.  You can remove the four
bolts from underneath the console, and just pull it out of the truck.
That'll make working much easier.  Heck, maybe even mount the tuner to the
frame of the console...  less holes in the floor that way  :)

On my '03, there was a nice deep channel between the top of the windshield
and the body.  I mounted the antenna ('mounted' is a strong word...  'stuck'
would be better, as it's a pretty powerful magnet) just below the center
marker light, and ran the wire inside that windshield groove (a little dab
of clear silicone kept it in place), and underneath the weatherstripping of
the driver's side door.  I cut a notch in the pinch-weld that the
weatherstripping grips, to pass the wire through (a dab of touch-up paint to
cover the bare metal, then a little more silicone to hold the wire in place,
and protect it from the edges), then ran it behind the dash.  If you mount
the receiver under the seat, you'd probably want to come down the B pillar.
The give you plenty of wire on the antenna, so you could even run it all the
way around the door's perimeter, underneath the weatherstripping, then under
the sill trim.

Another option some people go with is going through the 3rd brake light
(cutting a little notch in the escutcheon for the wire, and sealing it with
silicone).  I'm not a fan of that, mainly because it's more work to drop the
headliner in order to run the wire.