Once you have all of you pocket holes drilled you can start the assembly.
Take 2 legs and lay them down on the table. Then take 1 Top Skirt (Width) and 1 Bottom Skirt (Width) and place them between the two legs. I used two pieces of scrap wood cut to about 3/16" thick to leave a reveal where the skirt and the leg meet. Start with the top skirt and clamp the three pieces together and then you can screw them together. (I did not use glue for this part because gluing end grain to anything is pretty much useless.) Then repeat the clamping and screwing for the bottom skirt.
Repeat these steps for the other side of the desk using the remaining legs and Top & Botttom Skirt pieces.
I then added glue and plugs to the holes I made in the bottom skirt. Before I continued to part 2 of the assembly, I let these dry for approximately 30 minutes. Once dry I sanded them flush with the skirt using a belt sander. However I don't recommend a belt sander unless you have a lot of practice with one. It's very unstable and it is very easy to make a mistake. Another method is to use a router with a dado (or straight cutting) bit as pictured below.