Which iCloud account does iBooks use to sync?
The iBooks app on iOS as well as OS X Mavericks uses the account you use to sign into the iBooks Store for syncing bookmarks, notes, collections, highlights and purchased books. So if you share an Apple ID/iTunes Store Account for purchases from the iBooks Store, then the sync will affect all the users who share the account.

The iBooks sync is not based on one's individual iCloud account, which is used for iMessage, FaceTime, Mail, Calendar, etc.

See iBooks: How to sync iBooks between devices for more information.