Stain or no stain, it's your truck. Either way will not affect the way the varnish/varathane adheres to the wood! The biggest problem people run into is not spending enough time to do the job right. Everyone makes sure they coat the top and bottom, dont forget the sides - but make sure the ENDS are coated too!
The ends of a wood board will suck many more time the moisture than the top,bottom or side will. that said, if you put 4-5 coats on the top and bottom then put 8-10 on the ends. Follow this and your bed will look great for years.
As far as automotive clear on wood, will it work - yes. Will it hold up - no.

Last edited by 54barnfind; 11/10/2012 10:45 PM.

....David