All of the drawer box parts where cut, with the bottom dado cut. I started by drilling all of the pocket holes.
My standard box for utility drawers is 3/4″ ply with 1/4″ bottom. Since the box is made from plywood I do not worry about movement so the bottom dado can go on all four sides. Simple ! (I do loose fit the bottoms to make assembly easy.)
I purchased a 4×8 sheet of 1/4″ Sandeply from HD. They cut in in 32″ sections. I can handle that on my table saw, so the 16″x~32″ bottoms were easy.
My pocket hole assembly process always uses my double clamps. These are clamped to the workbench top and made square. This gives an excellent holding for the box parts. I added top clamps to make sure the joints are totally tight before putting in the pocket hole screws.