For future reference, please don't necro post old old threads. Always look at the last post date before replying to a thread. If it's more than three months ago, it's a dead thread and should not be responded to.
In the future, it is always better to reply to the stickies threads entitled "HELP! For XXXX", these are specialized places where super helpful people can easily look and see that someone has asked a question, and under which topic they asked. For instance, your question is a "HELP! For Pepakura" question, so placing it there would help us better answer. I would have probably seen this sooner if you'd posted in the right spot, as I check the HELP! For Pepakura/Bondo topics daily.
Since we're already here, I'll just answer, though. If you are getting everything crammed at the bottom, then probably your printer is struggling to feed the cardstock (assuming you're using it) through. The first step is to test this theory: Print off one page of your pepakura project on REGULAR PRINTER PAPER. If it goes without a hitch, then you know your printer can't handle the heavy cardstock. Your best bet is to either take it all to a kinkos/ups/other copy store (Either by exporting the pep to PDF, or printing it on regular paper to be copied onto cardstock) and having them print it on the right cardstock. Alternatively, find someone else who has a different type of printer and windows. I personally look for printers where you can load the paper in the back, rather than front, but some people have good luck with newer printers that load in the front too. If it's an office style printer (The ones with more things sticking out of them, including an ADF tray above the scanner) you will have better luck than with a cheap-o bargain printer. I hope this helps, if it does, or does not, please reply on the "HELP! For Pepakura" thread and not to this one, as we should lay this thread to rest now, I just figured since it was already on the first page, it'd be best to answer the question than leave you hanging.