I'm aware of this question but it is now quite old. If I create a collection in iBooks on OSX (Yosemite, 10.10.3) and add a book (epub - not puchased via iBooks), it does not sync to my iPad (3rd gen, iOS 8.2) over wifi. The name of the collection itself is synced to the iPad but it is empty. Both devices are on the same wireless LAN and connected to the internet.
I believe syncing used to be via iTunes and this was the only way I could get books to sync to my iPad previously but this should now work using only iBooks. I have already performed the 'Move books from iTunes' operation from the iBooks menu on OSX.
'Sync Collections' is switched on in the iPad iBooks settings. I'm looking for a wireless solution, not USB sync.