I think the trick to it is to put your dark shading layer on the bottom, with your pencil lines on top of that, and then paint your highlights on a layer above the lines. I usually end up merging the layers about halfway through, but that's the way they're set up when I start.
Thank YOU for buying it! What's your email address? I'll e-mail you the high-resolution image. If I had known that I was going to be coloring this, I would have included a print with your package, but it was a totally spur of the moment thing that came about after I'd already mailed it out.