I recently started using iBooks; I had the latest iOS(9.3.5) and OS X(10.11.5) versions. I mention the version because as I write this I have no idea whether this behavior still exists in the current version. When I turned on iBooks iCloud syncing in iCloud Drive Options and/or the first time I opened iBooks on either/both the Mac or iPhone for the first time since OS X 10.11.4 or iOS 9.3 all of the PDFs currently in my iCloud Drive in any folder were added to iBooks. This made me assume every time I put a PDF or "epub" document in my iCloud drive it would get added to iBooks. When I added additional items to my iCloud drive they didn't appear in iBooks. This totally confused me and I thought it wasn't woking correctly. Recently, I had moved my entire iCloud Drive from another Apple ID. (This involves commands in terminal.app.) I was afraid I broke something. I realized there were now two copies (1 hidden) of each PDF on the iCloud Drive. I could not figure this out. After reading carefully all the available documentation I realized the problem wasn't the fact that new items added to the iCloud drive weren't showing up in iBooks; the problem was the original transfer of all the PDFs to iBooks shouldn't have happened at all(this behavior is not documented anywhere). iBooks iCloud syncing is supposed to be invisible like all the other Apps, Apple and Third Party alike. With iCloud Drive syncing turned on, on all your devices, one just needs to drag an "epub" or PDF to iBooks and it will then sync with every device through iCloud. It is not meant to sync with items that were simply dragged to the iCloud Drive. When iBooks iCloud syncing first got turned on a duplicate PDF was created for every PDF in my iCloud Drive. All of the PDFs that are syncing between devices are located in "$HOME/library/Mobile Documents/iCloud~com~apple~iBooks/Documents". The best way to add a document is to drag it to iBooks. There is a way to drag items to iCloud Drive, it is just an invisible folder. If you drag items to this folder the item is moved, not copied. When you drag items to iBooks, those items are copied.
If you have no iCloud items synced with iBooks and you open the invisible folder, there is a nice message when you open the folder inviting you to drag iBooks content to it. So remember, when you drag something to your iCloud Drive it disappears from your computer if you logout of iCloud or turn off iCloud Drive. If you download a free book, Dracula(to old for Copyrights) for instance, and you drag it directly to the iBooks folder from Downloads(where it is now if you clicked on the link) then you won't have extra copies of the file hanging around.
To see all the iBooks items that are syncing with iCloud Drive, open a Terminal window and cut and paste this command:
open "$HOME/library/Mobile Documents/iCloud~com~apple~iBooks/Documents"
This is really just a folder with documents that are opened by iBooks not unlike the "Pages" folder on the iCloud Drive.
It is clear the implementation was undecided for a period of time shortly before the release of the update, bits and pieces that shouldn't exist got left behind.
So, if you wonder, like I did, why items dragged to your iCloud Drive don't sync with iBooks because they all did when you first turned it on, don't wonder any more, just drag them to iBooks.
Use iCloud Drive or iBooks to access your PDF files, ePub files, and books - Apple Support
