Once your user has finished filling the form data, you actually just want to export the data to XFDF(XML) and sent that to your server. The PDF file is left alone (this of course saves a lot of bandwidth, as the XFDF file will be much smaller then the PDF.
Essentially, you are just passing an XML string back to your server, and you can with it as you like, typically entered into a database. Or you can merge the data into the PDF server side.