Get a piece of paper and a pen (or marker board and markers if you want even more realistic practice). Draw out each square, 4x4. Then when you begin "unfolding" the paper, mark an X where each hole would be, & a O where there could be no whole. It goes alot quicker than you would think and helps you remember where each hole is.
Learn origami. I'm not joking. Find a site that gives you directions on how to make things, and follow along. The practice will help you get a better grasp in visualizing the folds on the actual hole punching.