Generally, if I'm working on a piece that has a lot of pages, I only cut out the pieces I'm going to be working with. I'll cut out parts that make up a small assembly, get them scored, folded and assembled, then put them onto the piece, then move on to cutting out the next group of pieces. That also helps in organization; I don't have a huge pile of cut out pieces that I have to sift through to find the right part. If the parts remain on the paper, I can refer to the model in Pepakura to find any given piece.