Export your Papers library with the command File > Export... > Refman RIS File. Save you entire library to a file on your desktop. Here is an example:
Now locate your Papers Library directory. Go to File > Preferences in the Papers menu. The location of your library will be listed in the Library tab of the Preferences window. Go to the library folder and find the Files folder within it. Keep this Files folder open for the next step.
In Paperpile open the menu, choose Upload Files and add both your exported RIS file and your entire Files folder to the upload dialog. Click Start upload to begin.
Paperpile will import your library and attach all existing PDFs to their correct articles when possible. When the import is complete, double-check any articles marked as incomplete or duplicates to help keep your library clean.