If I remember correctly with Stanza you don't load anything in iTunes, you put the stories in a folder on your pc and then when your iPad is connected you go to the Apps page for your iPad, scroll down, past the apps, then you get to a box which says 'these apps will allow you to load items onto the ipad' or something like that. Select Stanza, which should be listed, this is on the left, then in the blank box on the right you select something which allows you to navigate to your folder, you select your stories, and you can load tons at the same time, and they pop onto that box. It's something like this (it is 1am here, I am in bed and writing from memory)

Is that what you are doing to import your books into Stansa?