Step 5: File format for laser cutting.
So what to do from here? Open the exported EPS file you got from Pepakura and organize them into the Ponoko template. For other places I'm going to guess that you could make the document the size of the material you got and then organize the pieces on there.
Some suggestions for organizing the pieces. Try and get some of the pieces to share an edge to decrease cutting time. Make sure you don't have double lines, this could lead to the laser going over the spot again, which could widen the cut patch, making the pieces not as accurate as they're supposed to be.
Once this is done you can send it on the wherever and get them to cut your pieces out and ship them on to you. Once you get them, get the screws, springs, w/e you need for the putting together part and there you have it. ALL DONE!!