I don't know how to make design with Pepakura, but the numbers on every side of a model help you to fit each part (example: 515 from one part goes to 515 from the other part). Also if you point your mouse over a part of the template the program will show you where to match and glue the corresponding parts. But you might try to search on Google or YouTube for how-to-work-with-Pepakura.