With the release of iOS 9.3 and Mac OS X 10.11.4, it is now possible to sync your ePubs and PDFs across all your devices and keep the read positions and bookmarks up to date.
Set up is pretty straightforward if one only has one Apple ID to handle their store purchases and iCloud data, however it becomes a bit less clear if you use a shared Apple ID across the household for purchases with individual iCloud accounts to sync personal data.
Anecdotally, it seems like the optimal solution is to:
- Remain signed in to your shared Apple ID in the iBooks store in all your devices (in iOS there is only one place to sign in – the App Store and iTunes store page in Settings).
- Remain signed in to your personal iCloud account
- When the prompt asks to enable the iBooks in the Cloud library, do so.
- If it signs you into the iCloud account in iBooks, sign out and sign back into the shared account.