I've had this requirement before. What I ended up doing was saving a copy of the PDF in the LiveCycle form repository. To submit, you call a web service that sends the form data to your workflow. The first step of that workflow remerges the data with the LC repository version of the form and you have a "submitted" PDF. The only issue with this solution is that you have to manage two copies of the form.
A possible way to work around that: If the form your users will be retrieving exists in a fileshare or on a server in your network, and you LC server has access to it, you can have your workflow pick up the form from the same place as the users. That way you only have to manage one copy. There are some variables/requirements you'll have to address to make that work, though. I obviously don't know about your environment.
If you'd like to discuss this further, feel free to email me. I'd be glad to help.
Ryan D. Lunka
Cardinal Solutions Group
rlunka@cardinalsolutions.com