A couple of ideas come to mind…
. Formidable Form has a file upload field that may be used to organize and store the pdf on your server.
. Our development services can provide you with personalized customization of the plugin by adding an optional shortcode parameter that would save the PDF to a folder on the server, and provide organization of the PDFs if needed. If interested, please send an email to support at formidablepro2pdf dot com to receive a custom development offer.