I guess I'm unusual. I consider my Kobo temporary storage while I'm reading a book, so I keep 2 to 4 books on the Kobo at any time. It also makes the home screen easy to navigate and I don't use the shelfs at all.
I use Calibre for long term storage and organization, including tags to keep track of what I've read. I use Sigil to touch up epubs the way I want. Sideloading to the Kobo involves copying to my local server and then downloading via the Kobo browser.
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