What's the interface you are envisioning?

Something like a right-click option ("open with") in the context menu should be possible by associating your application to PDF (be by extension or by mime-type)

But I have to admit I never tried this again since W98 ...

UPDATE

Additionally PDF printer drivers normally allow to print to file. You could choose BUK's suggestion of a monitored shared drive as default destination. (just call it "SQL-Upload" or similar)

see also Win32::ChangeNotify for an alternative in monitoring a directory.