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It's best to treat the Calibre Library folder as a black box. Whatever goes on in there is for Calibre's uses only. Save and keep your books outside of the Calibre library folder if you like to exercise your own management of files.
That being said, you can use Calibre itself to send books to your device rather than Dragging and dropping. That will make it easier to keep a large number of books on device organized. And if you want, you'll be able to use the Kobo Extended Driver to upload the books in Kobo's own native format instead of epub. (It's debatable which is better, as both book formats have different pros and cons.)
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