The rule of thumb is as free and clear as possible. I don't think I'd mount it right next to the back of the cab, but that's your choice.
Any good trim shop worth their weight can make a seal for the antenna. Just remember these things: no matter the material used, if it gets wet, and you decide to transmit, it will effect the SWR; it may arc over; doubtful, but it might catch fire; and probably a few other things if I think about it.
I originally planned to mount my HiQ on the outside of the truck, similar to the way I installed it on my Acura. I still might do that, but I do a lot of playing around, and the thought of removing the front and left side bed panels made me rethink the mounting scenario.
In your case, you might want to use the outside of the bed, but I don't know if it is a slab side or step side, and that makes a difference.
There are some 300 photos of other installs in my Photo Gallery (which is now working correctly), and surely one of those will give you some ideas.
The first question you'd best ask yourself, are you willing to drill holes?