Actually, what I noticed is that the only thing you need to do (provided calibre is configured for
automatic metadata management) is:
1. Send books in question to the device.
1. Eject device
2. Disconnect USB cable
3. Wait for Kobo to process new books
4. Reconnect Kobo and allow calibre to sync metadata.
5. Eject device and enjoy.
This will both fix the small square book cover and simultaneously sync the correct series information, in the library views you'll see the name of the series and the index in a format like this:
<Book title>
<Series> - <Index>
<Author>
It seems that with the copying of books along with their metadata to the kobo reader the series information is ignored and/or erased after the initial processing and sometimes the cover isn't shown correctly. 2nd metadata-only sync should fix this...