How I manage books on Koreader
Basically I save all the epubs books in the epub folder on Kobo.
Next in calibre, select all the books then click
Save to disk > Save to disk in a single folder then choose
the directory epub in your Kobo.
Note: You might need to configure the behavior of save to disk,
mainly to uncheck the Save cover separately, as it is inconvenient
to have them lying around with your books. Here is my setup:
To make the process easier, I overide the shortcut s to
serve the purpose of saving to disk in a single folder.
Managing your books this way has a couple of benefits. One
of them, which is very important to me, is that any metadata
that you change via calibre such as author name, series,
title of the book are saved directly to your books in epub folder.