Is the tonneau cover hard, soft, roll up, folding?
I use a guide gear bed tent now but no cover.
If your cover is hard you'd have to disconnect the shocks and lift and secure the cover vertical. With the folding ones you may Be able to do it if the folded part will lay up against the rear window. Soft Rolling ones you should have no problem.
It would be easiest just to remove the cover at home when you want to use a bed tent.