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Originally Posted by meme
First - you can definitely see all the books on your Kindle and what collections they are in - and whether or not they are in Calibre - use Edit Collections.
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I'll give that a try again - I was afraid to use it, after I managed to end up with only the Calibre maintained collections last night. Of course, I was able to go back a few days and get a good JSON file to restore, then start over. Also, the last time I managed to get into the window (I was getting errors, for a while), I could see the collections created in Calibre, but no books; all I could seem to do was to delete collection names on the Kindle.
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Second, I think I'm confused 
If you really only have 2 collections
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LOL!
No, not only two (or only two pages). But, I ended up with the original collection name (no "_" in front) and the Calibre maintained one (with "_"). I have a field for the imported collections and use it to edit and create new (the really old version I had used had used my tags ... all of them, which created a huge mess; removing those, while not losing the assignment of non-Calibre collection books (a couple thousand, or so), has been a priority.
So, now I have two "SciFi" (and two Fantasy and two Currently_Reading, etc) collections and want to merge them, without copying the Kindle only books into Calibre.
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...and you gradually want to move to one collection that is Calibre managed, then you may want to:
1. Import Collections into Calibre into a custom column (e.g. "Kindle Collections") (only books that are in calibre will get the collection name put into the column)
2. Setup the plugin's Customize to Create collections based on your custom column
3. Run Preview (to test/check) then Create - only the names in the custom column will be updated.
4. Now when you import a book into Calibre you can add your collection name into the "Kindle Collections" column and run Create, and manually delete (using Edit Collections if you want) the entry in the Kindle-only collection.
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Which is what I have, so far...
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When using Create Collections, it will only update the names it finds in the columns you setup in Customize, and leave your Kindle-only collection names alone. To be extra safe, you can put the Kindle-only collection name in the "Never delete" text box on the Customize screen and it will never be modified (and will be ignored when checking for changes which will be helpful if you really do want to mix automatic and manual creation).
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So, it sounds like I am stuck with two of each collection, until I manage to copy those books into Calibre, process them to fix titles, metadata, etc, assign the "new" collection in the custom column, then export them back to the Kindle (is this step necessary?) in order to add them to the new collections.
What I cannot do (if I understand correctly): Leave 200+ books in the Kindle collection, add the Calibre maintained books to it, import the collections and then create on the Kindle ... as this would remove those 200+ books from the collection, as they are not in Calibre, so would not be added to the collection when it is created. Correct?
I don't want to mix manual and automatic creation, so much as use automatic creation, have no duplicate collection names (other than the "_") and have all my books in collections (whether downloaded from Amazon or managed by Calibre).
If I can't do that, it's ok. Just means a substantial amount of work before my collections are working again (darn those free books + the bad programming design that slows the Kindle as the number of books installed rises). I've been avoiding putting the DRM'd Kindle only books into Calibre, since they are useless to read there and can't be sent via wifi to the Kindle of my choice (or read on one of my other readers).