mollyf, you can just put your Calibre folder inside Dropbox or SugarSync on your main computer, and then all of your Calibre books will automatically be always available on all your phones and tablets as well, and no direct transfer between your computer and the iPad will ever be necessary. Then, when you access your Calibre books from the Dropbox app or SugarSync app on your iPad, you can choose whatever app you wish to read the book in. (I recommend Marvin.)
Letting Dropbox or SugarSync take care of Calibre is really the fastest way. You set it up once, and you can then forget all transfer worries once and for all.
