You can store your PDFs in iBooks by using the Export or Share function in iCloud Drive, DropBox, or Adobe Acrobat. View the file in one of these apps and do the following:
- iCloud Drive: Click the file in the list, click the Share icon (square box with up-arrow) in the upper right, choose "Import with iBooks". (make sure you have iBooks turned on in the iCloud Drive Settings on your mobile device)
- DropBox: Click the file in the list, click the "three dot" menu in the upper right, choose Export, choose "Open in...", choose "Import with iBooks"
- Acrobat: Open the file to view, tap to bring up menus at top and bottom. Choose the Share icon (square box with up-arrow) at the bottom, choose "Open in...", choose "Import with iBooks"
After the PDF shows up in your iBooks library, you may safely delete it from iCloud or DropBox if you wish--it is now stored in iBooks on your device.
NOTE: I did NOT turn on iCloud inside iBooks because it will immediately start uploading everything it can to the iCloud, which for me would have run out of storage since I have over 500 PDFs. This was done with my iPad running 10.2.1, I have not updated to 11.0.2 yet.