Even though Paperpile doesn’t yet have a mobile app, you can setup the amazing iPad PDF annotation app to sync with Paperpile’s Google Drive folder. Personally I just sync with the “starred” folder so that I’m not downloading all my PDFs to the iPad. This works really well. I recommend setting it up as a one-way sync so that any changes you make on the iPad won’t affect your Paperpile account.
For those who are interested, my complete workflow then exports my annotations from GoodReader to Evernote. I find this works really well. I just hope that the Paperpile mobile app is released soon as sometimes I would like to “star” an item that is not yet starred and I can’t yet do that on mobile.