In sharing files with (say with pc) iTunes is made use of. However, the file must be associated with an app. File sharing cannot be done with all the apps, as an example under iBooks. On the other hand file sharing is possible under documents. So the requirement is how to make iBooks file shareable.
iPad (3rd gen) Wi-Fi + Cellular, iOS 6
Only the developer of an app, i.e. Apple for the iBooks app, can make it support file sharing. If you want to copy books and/or PDFs to the iBooks app then you select the iPad on the left-hand sidebar of iTunes and use the Books tab on the right-hand side to select and sync them e.g. in a similar way that you use the Music tab for syncing music.
If you have other apps that don't support file sharing then presumably they support a different transfer method e.g. transfer via your wifi network, email, Dropbox etc
How do I make an app capable of file sharing under iTunes?
