So I found this location on my Mac:
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?