The only way to do that is manually. A PDF in a case like this is simply a file of images and there is no way to automatically convert them to a file. You may be able to use parts as underlays to help you convert but I do not guarantee that, either (especially never having used underlays).
I have been using PCS 10 to make several graphed afghans. and i am having lots of fun doing it. until i found the forum most of my work was trial and error. but i will try several items mentioned to see if it make my work easier.
I also have a dual purpose for this program. My mother cross-stitches and i will be scanning and charting pics for her work. She is the reason our county fair has a class "Cross-stitch picture from a picture"