The dealership I bought my truck put my spray-in beliner in. If I had done it, it would've been over the rails, however they only donen the inside of the bed. The rails that came with the bakflip however, have a foam rubber strip on them to keep them from scratching your bed rails, and the clamps only contact the inside...

These covers are awesome, they can tolerate a lot of weight on top of them also, Bak says 200 lbs of evenly distributed weight can be placed on top, I've used it as a bench at tailgate parties with no problems. The only thing I could see maybe an issue is if you're a little short, that last fold up to the cab can get heavy after a long day of work, luckily I got some heighth on me so it doesn't bother me too bad, but I could see shorter people struggle a little.