Originally Posted by davidfor
The other thing you can do, and I'm surprised taming didn't mention it, is to let calibre manage the shelves. To do this, let the device sync the new book. And add the epub version to calibre. At the next sync with calibre, the books should get matched and the shelves set up.
I thought the issue was that the OP was trying to avoid having kepub books of epubs she owned before buying a kobo device on the reader at all.
I do all of my management using calibre. I have the books I bought from Kobo as kepubs on the device, and backed up epubs in calibre. As David mentioned, unless there is a mismatch between the two titles, I can use the shelves just fine in calibre and whatever format is actually on the device ends up on the shelves.