Apple has released version 1.2 of iBooks, including a feature allowing you to subdivide your books into collections, such as 'Fiction' or 'Thrillers'.
There is already a
feature enhancement ticket requesting that calibre support this feature.
Calibre's iDevice driver communicates with the iDevice exclusively through iTunes automation, and it appears that iTunes does not currently support assigning books to collections - as far as I can tell, it can only be done directly on the device.
For now, that means it won't be possible to implement this feature within calibre.
G