Should be another hole above your that third one on your right-hand picture that has a nut secured behind it (back side of the stake pocket) for the tailgate hinge.
The cross-sill gets bolted with short bolts and nuts inside the cross sill on the lower pair, both front and back of the stake pocket. Just sandwiching the two layers of sheet metal, not all the way thru the stake pocket.
I think the same short bolts should be used on the upper hole, front and back, with the back top hole also holding the lower end of the tailgate hinge. It's been a while since I disassembled my bed for repairs, so not positive. You might check on Mar-K's site for assembly instructions.
