Will the 'back up to this computer' setting in iTunes allow for storage of PDF files, etc. (non-iBooks content) on my computer for later retrieval, if need be?

Question

Up until now, I have had the 'back up to iCloud' setting enabled in iTunes for my iOS devices. However, when I recently had to restore my devices 'as new', I discovered through the process that the only 'iBooks' app data that is stored in the cloud are basically iTunes book and Kindle(?) book data. None of the PDFs that I pulled off the web and stored in iBooks were backed up to iCloud.
If I change this setting to 'back up to my computer' will iTunes go ahead and back up those other PDFs, etc. on to my Mac or will I, going forward, have to make sure and back up all those items onto my Mac manually and individually?
*Note: I know about Docs in The Cloud with Pages and iWork on iOS and I use these services as well. This question, however is centering around iBooks and iCloud.

Answer 1

Syncing with your computer will delete data from his phone but you should be able to restore his backup.
iOS: How to back up
However, he won't be able to play music purchased under a different iTunes account than the one his phone is signed into.  He can change the account to yours, but any apps he purchased under his account will no longer update, and any purchases he makes will go on your account.