How do I transfer a PDF I've saved in iBooks from my iPhone 6 to my iPadPro?
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There are a couple of options.
If you're using iCloud Drive, opening iBooks, scrolling to the item (a PDF, ePub or book) and tapping on the Download icon will download the item to your library. If you're not currently using iCloud Drive you can always turn it on under Settings / iCloud / iCloud Drive.
Syncing through a Computer. If both devices are synced with the same computer, you could go into iTune's device's Settings and enable Sync Books. Then syncing both devices would share the item. Bear in mind that if iTunes is set to sync only selected books, you'll need to manually check the checkbox next to the PDF you want to sync.
Send the file attached to an Email. Attaching the PDF to an email, opening it from the other device and saving the PDF file into iBooks would do the trick, too.