Mounting an antenna, and getting good performance from it are both concerns... typically, if a significant portion of the antenna is below the body line, the performance will be compromised.
I have done three different things over the years:
The first was to simply buy a magnetic Wilson 1000 or 5000 and place it in the center of the roof. This will typically get you a 1. 5:1 (or better) SWR without too much tuning. Be forewarned, if you run power; it will cause the paint to bubble under the magnet... a 3-pill bubbled the paint on my 99 using a Wilson 5000 magnet mount. I didn't like this because you have the coax draped over the truck (not really a clean look).
I then decided, since I was keeping the truck for a long time, to drill the roof and install the through-roof mount for the Wilson 1000/5000. This will typically get you a 1:1 SWR because you have a direct contact with the body, not an induced ground from a magnet. With aftermarket coax, I've ran a 5-pill with good results on this setup. And for whatever reason, this is the best setup for skip in my experience. The Wilsons are a nice antenna in the fact the whip/load can be removed from the mount for clearance in garages, etc. .
I currently run a 102-inch whip and spacer (spacer in place of the required 6-inch spring) mounted on the front bed rail (dead center of the truck). I like this because the 102 is practically indestructible and stupidly simple... no coils, no capacitors, no snake oil. My SWR is 1:1 on all channels, even with almost two feet obstructed by the cab.
As for the radio, depending on what you want, look at the BigBob mounts from Geno's that mount to the center console. I ran one of these for a long time (still have a meter mounted to it). I currently have my radio mounted to the side of the hump, near the driver's right foot.
Attention: TDR Forum Junkies 
