With the slots cut in the upper board, the next step is to cut a pair of 1/2" diameter holes in the lower plywood. Each of the two hex bolts will go through these holes, then through the slots, which will allow the jig to joint various widths of boards.
On your shop table, position the upper board onto the lower plywood, centered on the long axis (about six inches in from each end), and 2-1/2" in from the right edge of the lower plywood.
Then, using your pencil, make a mark through each slot at the left end of the slots onto the plywood below. Remove the upper board, and then drill a clean 1/2" hole through the plywood at each of these two pencil marks.