I wouldn't recommend using backups as a synchronisation method. It's too cumbersome and backup files will tend to grow large as you add more books to your library. Of course you can send backups to Dropbox (or any other cloud app) to keep "cloud" backups.
The sync option is to synchronise your reading location between devices. I wrote something about it here:
http://blog.marvinapp.com/post/61407972806