First off, what app are you using? The Official Apple iBooks app is nasty in that it allows no upload or download of its contents (bookshelf). However, with Adobe's Reader app, an "File Sharing" section opens up in the bottom portion of the Apps pane for your phone in iTunes, in which you can transfer content for that app. Transfer is bidirectional.
Then there's the Disk Aid application you run on your Mac, that purports to let you munge all sorts of stuff on your phone. Have not tried that. http://www.digidna.net/diskaid#appsIntLnk
"Transfer Purchases" is quite totalitarian. All or nothing. Causes the phone to sync up with iTunes, like it or not/