In addition to Sharing with Stanza Desktop, and uploading/downloading books, you can also use Calibre, the free e-book application for Windows, Mac and Linux, to transfer books to Stanza iPhone. Here are a few links to instructions for how to do this:

http://calibre-ebook.com/user_manual/faq.html#how-do-i-use-app-with-my-i...
http://www.mobileread.com/forums/showthread.php?p=391919#post391919

There is also a user-written tool called calibre2opds to help manage your Calibre library using Dropbox, described at:

http://www.mobileread.com/forums/showthread.php?t=64095
http://www.mobileread.com/forums/showthread.php?t=62332