Apple - Can I get non-iBooks Store ePub files into my iCloud iBooks library?
You can email yourself the files, then from Mail, open the files in iBooks.
No, that doesn't work: there is no iCloud sync of the entire ebook file. The only thing that is possible with non-iBooks store ebooks is to sync the reading location and notes.
So, if you load an ePub file into iTunes/iBooks on a Mac and then sync it via iTunes to your iOS device(s), and if you have the sync option activated in all of them, the reading position and notes/highlights/bookmarks will be synchronized across them.
Note that in fact that's what happens with the purchased iBooks: it's not that Apple is saving your books on iCloud, just the record of your purchase.
This functionality will be support beginning with iOS 9.3. It will support syncing the entire library, including PDFs on any device.
Here is the Apple Support page with documentation: https://support.apple.com/en-us/HT205751
Federico Viticci mentioned this on Twitter first.