Booxstor's advice works fine. I've tested it on scanned car manual, few days ago.
Other solution would be to cut the double page doc into single page doc. There is sw for such pdf manipulation.
You may try it. SQL file for each document is stored in .onyx folder. The database file has the same name as document file (extension is different).
Make few annotations/bookmarks and then remove/rename the SQL file. If annotations/bookmarks disapear, they were in the file.
If not, they are somewhere else.