I looked at the instructions, and you are correct. On each 50064 bracket, you have one bolt towards the rear of the truck which is a 3/4" x 2" with its associated washers and nut.
Then, on the front of the bracket, you have a choice of two 1/2" x 4-1/2", or 1/2" x 5-1/2" bolts depending on your truck. Also, depending on your model, you'll install a spacer between the bracket and the rail at the front of the bracket if needed.
So, on each bracket, you have three bolts. I also see that you should have 5 bolts on each rail. Two on each outside edge, and one in the center that bolts through the bed (no bracket, just a conical washer).