Step 5: Phase IV - Organize
1) First, merge as many of the tiny, sliver-like pieces with long corresponding edges as you can. Just imagine having to cut those little beasts out later on if you don't! Do whatever you must to keep pieces and corners from overlapping as you merge and dissect the shapes. Sometimes, you just can't help but leave a tiny piece by itself, however in these cases, it is helpful to keep them always adjacent to where they're supposed to go.
2) Find the symmetry. And don't worry about keeping the pieces smaller than the page limitations just yet; that will be the easy part later on. For now, just focus on making sense of this mess. What I mean is connect as many pieces together as you can, and keep rearranging them until a [mostly] symmetrical pattern emerges with parts that you can start to recognize where they will be in the structure of the finished papercraft. I say 'mostly' symmetrical because hairdos that generally appear to be symmetrical may not actually be so once you take a closer look, thus a perfectly symmetrical flat layout would be impossible. You can still come close, though. It just helps to simplify things in the build stage.
3) Once you are satisfied with your work in Step 2, select all of your pieces and drag them down to the bottom of the view field into a pile. Select one, and begin dissecting it into pieces that will fit within the page boarders. Organize these smaller pieces into the pages at the top of the view field. Do this systematically for the whole pile.
4) Now would be a good time to save your work if you have the .pdo export feature. (Pepakura's native file format which is unlocked when you buy a passcode from the developer.) If you still just have the free version, don't forget about CutePDF Writer! At least you'll be able to save your work in some form rather than not at all. Tip: In the later scenario, save multiple versions of your template, i. e. one .pdf with the texture file turned on and Edge ID numbers turned off, and one .pdf with the texture turned off and the Edge ID numbers turned on, etc...
....CONTINUE TO NEXT PHASE!