Looks like in iTunes 12, books have been removed totally, only audiobooks section showing.
How do we import books to copy to iPad now, that have not been purchased under iTunes?! iBooks app does not appear to have the functionality.
I presume there is going to be an iBooks update for when Yosemite/iTunes 12 launches, but guessing until then, got to try another way?
Unless I'm missing something....?
Looks like this post is 3 years old. I'm hoping you've found the solution by now. I've been plagued by the same confusion as I'm a new iPad user and have been trying to transfer EPUB files from my PC to my new iPad with no success. I, too, have been using the latest iTunes (12.7.2.60) and have come up with the same questions. I've also found little to no help from Apple Tech Support (my dog seems to know more about Apple products than they do). But after much reading, researching, frustration, and a little luck I've come upon the following solution...
You CAN transfer your EPUB and PDF files from your PC to your iPhone/iPad through iTunes! You are correct in that there IS NO "Books" folder within the iTunes library (makes the process very frustrating when people say, "just use iTunes"), however, when you connect your iPhone/iPad to your PC and access the device contents via iTunes, "Books" is one of the folders listed under "My Device" on the left-hand window. You can select that folder, so the contents are shown in the main window, and drag your eBooks from the folder they reside in on your PC directly into this folder in iTunes. This utilizes iTunes as the transfer media while not saving your eBooks to the iTunes library. The only problem I encountered with this process is that it won't transfer MOBI files - the error message said the device (iPad) won't recognize that file type.
Hope this helps.