Apple - Sync books from iBooks on Mac with iBooks on iPhone
In short, the iBooks application and its behavior were kind of a big surprise to everybody. Before I opened it, Mavericks seemed great.
The iBooks application seems positioned to deal only with purchased (DRM) books. This includes your ePubs and PDFs. It wasn't announced, but it seems to be the case. Also the iBooks application on the desktop isn't intended to be the means to sync to your iDevices. When you sync your device, the iTunes "Books" selections will come from the new iBooks application.
All of your not-purchaed ePubs and PDFs that you used to store and sync in iTunes, well now you have to use something else, like Calibre. Whether or not this continues to be the case is unknown. It's possible that the new iBooks app is an attempt to distance Apple from non purchased books.
I spent a day putting all my non-purchased books into Calibre and it works fine. It's not seamless with the syncing, especially if you used to do it over WiFi. For the moment that capability is not available. Calibre has multiple methods for copying to devices, and you will definitely need to do a little digging in the documentation.
So for the moment, you have two separate methods of syncing books: iBooks and iTunes for purchased, and Calibre (or whatever) for non-purchased.
When you start iBooks for the first time, your iTunes books will be transferred to a folder buried out-of-sight. Most of the ePub metadata will be in the ePub file, but not so for PDFs. If you were lucky you copied your stuff out of iTunes before using iBooks. I wasn't so lucky.
BTW, any PDFs that are music booklets (or in my case, sheet music) can stay with the album in iTunes. However they are media type "Music".
It is possible to sync notes/annotations of 3rd party EPUBs using iBooks for Mac & iBooks for iOS, but the EPUB files themselves do not sync. Weird, but true.
(1) Keep your 3rd party EPUBs centrally in Dropbox, so it can be "accessed" from any Mac or iOS device. (You can also host these on a private web-page on your LAN. I use papaya app from lightheadsw.com for this.)
(2) Open the EPUB on each Mac and iOS device, from the Dropbox folder. This creates a copy of the EPUB in each of the iBooks apps.
(3) Last read position, highlights & notes that you make on the EPUB on any Mac or iOS device will be synced across all other devices -- provided you've signed into iBooks store using the same Apple ID on all these devices. And you've checked the sync bookmarks/notes setting in iBooks.
Points to note:
iBooks doesn't sync data using your iCloud account, it does so using the "store-linked" apple ID. Think of iBooks as an extension of iTunes. It doesn't behave like Pages/Keynote/Numbers etc which use iCloud for documents sync. it behaves like iTunes Match which uses your store account for ratings/metadata sync.
The EPUB itself is not synced by iBooks - only the highlights/notes are synced. When you insert the same EPUB into iBooks for Mac and iBooks for iOS, it tries to match the EPUB against notes/annotations stored in the cloud, and if there's a match, then notes will show up on that device. Thus, it's important to take the exact same EPUB and open it on iBooks on Mac, iPhone, iPad for notes sync to work. Think of an EPUB as read-only, including the filename, and that you need to manually insert it into every copy of iBooks.