New update on itunes- no file transfer in adobe reader?

I can not tranfer files from my computer into adobe reader on my ipad in the new itunes. There is no longer a left hand menu to go to apps and the new menu under apps just shows your apps but does not give any options for transfer.. please help. I transfered into ibooks first but need to take notes. Since the new update has changed itunes I can not find the options to trasfer my files.