Noise
Hi Big Mak, you shouldn't have any problems with the spray-on bedliner from the stacks if you maintain an air-gap between the pipes and the bed. The only time I've heard of or had any heat issues are with the original bedliner and running very high temps for hours on the highway.
The sound of stacks depends on your tollerance for noise. If you don't mind some constant exhaust sound, you will be happy. If you prefer no exhaust sound then the stacks will seem noisy or loud. It is worse in the back of a club cab.
There are many methods to quiet your truck if you are concered about noise, even with stacks. Send me a PM if you are interested in discussing custom stacks or Noise Issues
Greg L. The Noise Nazi