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With Kobo while you can add books to collections on the device itself, it is far easier (if you use calibre) to manage collections via calibre.
If you do decide to manage via calibre, make calibre the canonical source for collection management; changes made on the device itself will be discarded by calibre.
Changes can be made via calibre, and on the next connection of your device to calibre will be automatically updated.
A book can belong to as many collections as you want, however there is no means (either on the device or in calibre) to tell what books are not in a collection.
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