How to copy pdf files to be view with iBooks on iPad using iTunes So I found this location on my Mac:

~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/Books

I then copy pdf files to that location.  In iTunes, from the left column under Settings I clicked on Books.  On the right view I can see a list of books that I downloaded from AppStore and pdf files that I downloaded directly using Safari on my iPad.  But I do not see any pdf files that I just copied to the Mac location above.

So how do I transfer pdf files that I have manually to my iPad without using Safari to download?
Might need a bit more info on what you're trying to do and what gear you're using but if you're on Yosemite then just open the iBooks app on your Mac then drag your pdfs into that. Then connect your iPad and open iTunes. Select your iPad in iTunes then select the Books tab and make sure Sync Books is ticked and All Books selected. Then sync your device. Alternatively, you can use Adobe's PDF Reader app or one of the many other PDF apps for iPad and use iTunes File Sharing to copy the PDFs across.