ibooks not showing up in itunes

I am having a problem with syncing books onto my iPad. When I open up iBooks it shows that I have 70 books, but when I try to sync these books onto my iPad through iTunes it only shows 10 books. The format for all these books are ePub and they were not bought through the iBooks store. I've had this problem before, but I cannot remember how I fixed it. I've tried clicking and dragging the files into iTunes, but that did not work. I can see all of the ePub files through finder home > music > itunes > itunes media > books.

OS X Yosemite 10.10.5

MacBook Pro (13-inch, Mid 2010)

iBooks 1.2 (825)

iTunes 12.3.0.44

iPad Air iOS 9.0.2