The short answer is... you can't.
The best you can hope for with the synchronization of non-Amazon content is the "furthest page read." Highlights, bookmarks and annotations will only sync across devices with Amazon purchased content.
To manually transfer the clippings??? I don't know... it may be possible. It might be tied in with the companion .mbp file.
Last edited by DiapDealer; 02-07-2011 at 08:57 AM.