I agree w/ alot of what you said. My advice, put everything in collections. I've created extra collections called "read", "not read", fiction, nonfiction, science fiction, etc., so every book has a place; and many books are in more than one collection.
RE: Collection Manager, my work flow seems to be:
1 put books in collections on the Kindle, using the Kindle manually
2 import Kindle Collections into Calibre, using the manager plugin
3 mirror (save) all my books on the Kindle, into Calibre
This is only difficult to do the first time; adding new books is now easy and fast (via calibre).
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