but I can only recommend for folks to avoid iTunes altogether
when transferring books to their iPads. There are lots
faster, simpler ways.
My method: I let SugarSync mirror all my Calibre folders online. That way, I only need to open the SugarSync app on my iPad, and open any book (any EPUB file) from any Calibre folder right there. You get a choice of e-reader apps: Marvin, Stanza, Bluefire, ShuBook, whatever!
You can also let Dropbox do the same. (By putting your Calibre library inside Dropbox.)
Another quick method (much quicker than iTunes) is just to email any book to yourself. You can then select Marvin, Stanza (etc.) for opening the book from the email attachment.
And finally, starting from Marvin version 1.2, you can also access your Calibre OPDS catalogue directly from Marvin.
Given all these fast, hassle-free, wireless options to get books onto your iPad, I wonder who would go through the torture of physically connecting their iPad to another computer, and then wrestling with iTunes...
But, to each their own.