I have a 2012 crew cab with ram boxes and purchased a bakflip F1 (3 piece) tonneau cover and am VERY satisfied with it. I believe Mopar makes one also for the ramboxes but the dealer commented on how my bakflip fits much nicer on the truck than the mopar one does and after seeing both, I agree. It looks like it's part of the truck.
here's a link to their website and a pic of my Ram with the tonneau.
hope this helps.