You can create pdfs/ibooks in iBooks author (http://www.apple.com/ibooks-author/) and them transfer them over, but obviously it's a mac only program. I'm sure theres an adobe reader app somewhere, so could place them in a dropbox folder and then view them that way. I recently moved to a nexus tablet so am out of the loop…
If I am not mistaken, the "official" way of doing things is as follows : PDFs get added to the books category in iTunes on a Mac or PC. Movie files (preferably already encoded in an ipad-friendly format and codec - use the free PC program Handbrake for that) are imported as movies, also in iTunes, on a Mac or PC. If you…