To sync eBooks (ePub and PDF) via USB:
1. Make sure the eBook is in the iBooks library.
2. Connect the iOS device to your computer via USB.
3. Open iTunes and select the device, then select Books.
4. Make sure "sync books" is selected and choose either the "all books" or "selected books" radio buttons. If you select "selected books" you'll need to then also select the eBooks to sync.
5. Click the Sync button.
This method also works for eBooks not purchased from the iTunes Store and over Wi Fi sync.