Hi Larry - you could square it up by playing with the screw tension but you would be sacrificing joint tightness. You would also need to make sure your design had plenty of redundant bracing to ensure rigidity and I don't think glue would be optional. You may also be able to "cheat" a bit with shims. To follow your thoughts, put the first screw in the tight side and make sure it is tight. Square it up and shim the "loose" edge and put in the second screw tightly. Trim the shim leaving part in the joint.
Thanks John for the suggestion. Clearly square cuts are very important just as getting the right lengths are. I will work on my accuracy and maybe that is the only way to square up a frame if one is using the pocket hole technique. I was hoping there was another way in the case where the cut is a little off. For example what if I only joined each joint with one screw and did not pull it tight. Then couldn't I check the square just like I would if I was not using pocket holes, or would the frame just move when I went back and added the second screw and pulled the screws tight?