JT,
In Pepakura Designer there's an icon that looks like like a blue square with a zip. If you click on this icon, in the 2D view if you click on the edges when they are green it will "unzip" them, if the line is red when you click it, it'll reattach it to the adjoining edge.
If you want to make your own paper models from a 3D computer model. You can use this software
Ultimate Unwrap 3D - UV mapping software to unwrap the model and make texturing in photoshop easier.
Hope that helps,
Alan