You could utilize the Zend Framework's PDF library to create, modify and save PDFs. Otherwise there is a PECL extension called [man]pdf[/man] which will let you do the same thing.
As for uploading it, if you're doing this on your server, where do you need to upload it to? Or do you mean download it? So after a user submits the form, they get a PDF back? Or after they submit the form, the PDF is stored elsewhere.
Storing it elsewhere can be done in one of a few ways. There's [man]ftp[/man] functions that you can use, or you can use rsync or scp if you have ssh access to both servers. And you could even use mv or cp if you're on your own dedicated server.
Sending the document back to the user is simple enough. When you're ready to send it back, make sure that you haven't sent content yet and set the Content-Type header, then just echo out the pdf string.
<?php
// After processing ...
if(!headers_sent())
{
header('Content-Type: application/pdf');
echo $myPDFcontents;
exit;
}
// Some error stuff
echo 'We tried to send you the pdf, but the headers were already sent?';
Hope that helps.