To sync a PDF from your computer to iBooks on your iPhone, iPad, or iPod touch: 1  Select your iOS device. 2  Click the Books tab. 3  Select Sync Books. 4  If iTunes is set to sync only selected books, select the checkbox next to the PDF you want to sync. 5  Click Sync.f you are using Manually Manage Music or Videos, disable the option in the Syncing Summary tab. To sync a PDF from your computer to iBooks on your iPhone, iPad, or iPod touch: 1  Select your iOS device. ( 2 Learn how to sync your data with iTunes 3  .). Click the Books tab. 4  Select Sync Books.