Audiobook Builder will automatically add a file to iTunes after the Build process has been completed. So, check the Audiobooks section or the Audiobook Builder Playlist for the file in question.
When you're ready to sync a new Audiobook to the iPhone, just connect to the phone, select it from the Devices area in the iTunes sidebar, and then click the Books button at top of the window to choose the 'Sync Audiobooks' option there. For more information on this process, check Apple's Help here:
http://support.apple.com/kb/PH13696