Here are a few tips that may help, which I believe are covered in the in-app help book as well (namely, Settings gear > Help > Syncing Documents > Sync with Dropbox)
1. PlainText only works with, well, plain text files (*.txt). It does not handle rich text like .rtf or .doc. If there are other, non-plain text files in folders, PlainText won't display or sync with them.
2. PlainText syncs to a single folder in your Dropbox, and any folders inside that one. By default, that's the PlainText folder.
3. You can choose the folder you want to sync to when you're unlinked from Dropbox. Just edit the "Link Folder" path to what you want. If you want the entire Dropbox folder to be accessible, just use "/" as your Link Folder path.