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If you want to manage arbitrary collections, doing it directly on the Kobo via the regular user interface might be easiest.
What Calibre's Kobo addon and my AutoShelf mod do is automate collections entirely. In Calibre you can do this based on author, genre, series (or whichever metadata fields you desire), for AutoShelf it's based on your directory structure.
Basically if there is a rule to the way you create collections, you should automate it. Once automated no need to intervene manually on the Kobo or in Calibre.
If you have no rules but collections like "Books I enjoyed" or "Books I hate", or "Books I want to read this year", the manual way of doing things might be fine. To achieve the same thing in Calibre you might have to add custom metadata columns.
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