Wired has a detailed article on how you can extract the contents of Stanza on your iPhone and move it to your iPad. Their instructions are both technically accurate and easy to understand.
One point they should have made, but didn't, is that you should be using calibre to organize your content. It can act as a server for Stanza over a Wifi network. Now that Stanza is kinda working on a jailbroken iPad, I strongly urge you to leave your content in calibre.
BTW, once again I'm appalled at the hoops Apple makes you jump through just to move your content around (but that's beside the point).