Originally Posted by rebarnmom
Now how do I get the duplicate collections merged together with the original?
Maybe you should try removing the collections that you've made already.
Right click the collection in the library, and delete. It won't delete the books in them, because they are only duplicated to be put in the collection (so your book will be in two places at once, and if you transfer the collection to the Reader the same applies). Then create a new collection with the "plus" button at the bottom left of the screen. I'd do all of this with the Reader not connected.