We don't recommend using GoodReader. Actually we strongly advise against using the Google Drive syncing feature of this program. The reason is that it does not sync files correctly. If you locally annotate a PDF on your iPad and try to sync it back to Google Drive, GoodReader deletes the original file and uploads a new file with the same name. What that means is that it effectively deletes your Paperpile files because Paperpile can't use of the uploaded file by Goodreader.
We had a user who ended up very frustrated because every time he annotated a PDF he could not open it in Paperpile any more.
We don't officially support any third party apps, but I've tried iAnnotate and this program gets the syncing right (and seems to be much easier to work with in general).