Guys,
Just to make it all clear (and I think Apple did a lousy job explaining it), the SYNC function on your iOS device is meant to ONLY sync bookmarks and the page number you're at now between iBooks on your Mac and the iBooks on your iOS devices. Nothing more nothing less.
It does not mean that the sync function on your iOS device will copy the books/pdf's from your Mac to your iOS device.
If you want to put a copy of a book/pdf you have on iBooks on your Mac on one of your iOS devices you must:
1) Open iTunes
2) Connect iOS device (cable or wi-fi)
3) In iTunes select the device you want to copy the books/pdf's to
4) After you selected your iOS device in iTunes, you'll see a number of tabs, select the "Books" tab. There you'll see all Books that you have on iBooks on your Mac
5) Proceed by checking all the books you'd like to have on your iOS device
6) This is kind of silly and I can understand it's confusing because now you'll have to click on sync to sync your iOS device with iTunes and get all books you checked at step 5 on your iOS device.
I hope this explaination helps a little.