Q: Since I’ve upgraded to OS X 10.9 Mavericks, I notice that iTunes no longer has a Books section; all the books have moved to iBooks. Under this new scheme, how do I sync books to my iPhone or iPad?
You’re correct that since Mavericks has an iBooks app, you’ll find that iTunes no longer stores your books. The first time you select the Books library in iTunes, the app will offer to take you to iBooks, which will then import your books. It will not, however, move your audiobooks; these stay in iTunes, and the Books library gets renamed Audiobooks. While iBooks stores the books, iTunes still manages syncing to your iOS devices. When you connect an iOS device and click it, you’ll see a Books tab, where you can choose what to sync. This tab manages the syncing of both ebooks—those stored in the iBooks app—and audiobooks, which are still in iTunes, just as before.
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Of iTunes and iBooks | Macworld
http://www.macworld.com/article/2061194/of-itunes-and-ibooks.html