The reason why it's asking you to transfer purchases is because your Mac doesn't have the apps (and the data associated with said apps (e.g.: game data, documents, etc).) on file on the computer. When it's transferred, it can successfully back it up without losing your data.
As far as I can tell, there is no way around it; you are going to have transfer the files. After that, go to the "Apps" tab on your iPad section of iTunes and uncheck it. This should stop syncing your apps. Do the same with the "Books" section.
As for the question of whether or not your apps and books are on iCloud, they are. Every song, album, music video, TV show, app, or book that you have downloaded is associated with your Apple ID and can be re-downloaded for no extra charge.
I hope that this solves your issue.
There are two ways to synchronize your own eBooks/PDFs between iBooks on the Mac and iBooks on an iOS device.
- using iTunes
- using iCloud
Short answer: synchronising own eBooks/PDFs doesn't work when iCloud synchronising is turned on on the Mac but not on the iOS device.
Long answer and my experience:
Problem 1: my own eBooks/PDFs were not visible in iTunes
Reason: on the Mac -> System preferences -> iCloud -> iCloud Drive there is a checkmark for iBooks.app.
When this checkmark is checked, iTunes is no longer responsible to synchronise own eBooks/PDFs.
Problem 2: I didn't get my own eBooks/PDFs in my iPad/iPhone
Reason: I did not have the iCloud Drive App from Apple on my iPad.
After downloading the iCloud Drive App, there are a few new options in the iOS preferences:
Preferences -> iCloud ->
- iCloud Drive
- iBooks
- and many more
This iBooks option is not available, when the iCloud Drive App is not installed and turned on.
After turning on the iClod Drive option and (after a few seconds) the iBooks option and then starting iBooks, iBooks will ask if you want to use iCloud.
After saying yes, all the own eBooks and PDFs are available for download one by one and controlled from th iOS device.
Best Answer
In Yosemite, this is now possible using only iBooks. On your iOS device (in my case an iPad 3rd Gen running iOS8), enable 'sync collections' in the settings for iBooks (within the iOS Settings app).
On your Mac, create a collection and add a PDF to it. It should then appear on your iDevice.