To begin cutting a box joint, you'll need the two pieces of stock into which you'll be cutting the joint. Typically, these two pieces of stock will be the same thickness and width, as in two corresponding sides of a drawer box.
Before making the first cut, you'll need to adjust the depth of the stacked dado blade on the table saw to match the thickness of the stock being cut. For instance, if you built the jig to have 1/2" wide fingers, but the boards being cut are 3/4" thick, you'll need to raise the blade to match the thickness of the board.
To make the first cut, position the board on edge so that the end edge of the board that will be cut is flat on the table. Slide the board to the right so that it butts up against the spacer block, leaving the edge flat against the table. After verifying that the board is extending upward square to the table saw face, clamp the board against the jig with a small woodworking clamp. Notice the picture above as an example.
Turn on the table saw and push the jig all the way through the stacked dado blade. This first cut will cut a new notch in the jig in addition to cutting the board. After the jig clears the blade completely, pull the jig back toward your body past the blade again and turn off the saw.
TIP: For good measure, add about 1/64" of an inch to the height of the blade so that when the box joint is assembled, the fingers will be slightly proud of the mated surface, ensuring a complete joint. This slight extension can be sanded after the final assembly of the box joint.