Apply clamps on both sides. When you put the first one on, be sure not to tighten it too much as this can cause the other side to spring apart. Put the clamp on lightly then put the next one on the opposite side, tighten them both incrementally until you have even pressure on both sides.
Use your rail to mark the width that mortise hole needs to be, do this on both sides. Mark the internal corner to give you the start and stop of your mortise hole. Repeat these steps for your middle shelf and the bottom rail.
On the side piece, the mortise hole will line up with the middle shelf recess, set your gauge to a ½“ (13mm) chisel. Run the gauge pins down into the recess you have just made. Use the same gauge setting to mark the other mortise hole further down on the same face.
Use the width of the rail to mark how long the mortise hole will be, square across and mark with a knife wall.