When using the "Perfect Layers" system, sometimes you can't get you tool to catch the edge of your paper for correct lining up, this is what I do:
1) Adhere picture (or paper) to the paper you need to cut.
2) Using your thumb, "fray" the edge a little away from the bottom piece of paper (just a little, it won't cause your picture or paper to stay that way)
3) Then the "Perfect Layers" tool will lay easily against the edge of your photo or paper.