When you make the pieces bigger, they need more paper to be printed on, and some pieces will have to use two pieces of paper. BUT, with Pepakura Designer 3, which I use, and with probably any pepakura designer, you can change the placement of the piece on the page. IT's like an annoying game of tetris until you get the hang of it. Just try it out and experiment with it, and you'll catch on. I just printed an ODST helmet, and had to change the size to 260 mm, (which was just barely too small X( ) and had to re arrange almost all the pieces.
You'll also want to make sure that all the pieces fit on the page, or else you'll have some wicked crazy issues with printing. just take your time and make sure all the pieces fit together, but don't touch each other, and you'll be fine. Hope this helps.