Officially, Ram recommends you don't use a fifth wheel hitch when you have RamBoxes. The limited bed clearance limits the turning radius of a standard pin box before it hits the sides of the RamBoxes.
Now that the disclaimer is out of the way...
Among some of the Ram sites I have seen people towing fifth wheels with Ramboxes. The key is to use the Reese Revolution or Sidewinder pin box. This changes the pivot point out the trailer instead of at the hitch, so it no longer rotates within the bed of the truck. Using one of those yes, you could use a foldable tonneau cover, as long as it fold far enough forward to expose the hitch.
As far as opening the RamBoxes themselves, it will depend on how much bed to trailer clearance you have, but it should be feasible. A quick google search turned up this:
Towing a 5th Wheel with RAM 2500 Short Bed with RAMBOX - Dodge Cummins Diesel Forum