I cut the plywood using my circular saw and the Kreg Rip cut. I did not cut the storage lid and the drawer front until the rest of the frame was built. That way I could make sure, they fit perfectly. .
Refer to schematics in the plans for locations of pocket holes. If you have never used a Kreg Jig before, check out my How to use a Kreg Jig post to get answers to all your questions.