Hello there, blackxacto.
It sounds like you are wanting to sync PDF's to your iPad Air without using the iCloud service. The following Knowledge Base article offers up some great information on that:
Use iBooks with PDF documents on your iPhone, iPad, or iPod touch
The first time that you open iBooks after you update to iOS 9.3 or OS X 10.11.4, you'll be prompted to use iCloud. Learn more about syncing your books and PDFs using iCloud.
You can also add PDFs to your iTunes library on your computer by dragging and dropping the PDF into your iTunes Book library. The files will appear when you are preparing your device to sync. If you're using OS X Mavericks or later, drag and drop your PDFs into your iBooks library using iBooks for Mac. All PDF or iBook files in your iBooks library are available to sync to your iOS device via iTunes.
To sync a PDF from your computer to iBooks on your iPhone, iPad, or iPod touch:
- Select your iOS device. (Learn how to sync your data with iTunes.)
- Under Settings, click Books.
- Select Sync Books.
- If iTunes is set to sync only selected books, make sure that there's a check in the checkbox next to the PDF you want to sync.
- Click Sync.
You can also use iTunes to back up your PDF files. To transfer PDFs to your computer and back them up, transfer purchases from your iOS device to your computer. These files are not in an iTunes Backup. Learn more about what's contained in iTunes and iCloud backups.
There is some additional information in regards to PDF and compatibility found here:
About iBooks
iBooks supports the ePub file format, PDFs, MP3 audiobooks, AAC audiobooks, and audible.com audiobooks. iBooks Author books are supported in iBooks 2.0 or later on iPad, iBooks 4.3 or later on iPhone and iPod touch, and on all versions of iBooks for Mac. Audiobooks are supported in iBooks 4.3 or later on iPhone, iPad, and iPod touch.
If you want to add books, audiobooks, and PDFs from outside the iBooks Store or audible.comto iBooks, they need to be DRM-free. You can sync them using iTunes 10.5.3 or later. Some PDFs might not be compatible with iBooks.
Books that you download from the Kindle Store and other books that aren't in a DRM-free standard ePub format aren't compatible with iBooks.
Thanks for reaching out to Apple Support Communities.
Kind Regards.