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Yep, ePUB is basically a zip file with the extension changed to .epub containing some text, xml and xhtml files. True, there's a lack of free/inexpensive editors/creator, but it's possible to make one using just notepad (or other plain text editor) and a zip creator assuming you have some knowledge of XML and XHTML.
First things first, though. How are you copying the created files over to Stanza for iPhone/iPod Touch? Instead of using Stanza Desktop, I would suggest using Calibre's content server, instead. Second, Stanza iPhone, is set not to display styles by default. You can change that by going to Settings » Layout » Display Styles while inside the ebook. Third, don't use just Stanza to test your ePUB. It's not really the best at ePUB rendering and coupled with the iPhone's small screen, well you get the picture. I suggest installing Adobe Digital Editions so you can view your ePUB files on the desktop.
As for getting the ebooks into Stanza, that's one of the easier parts, assuming the publisher has a web server where he can host the files. If you change the link to the ePUB file from http:// to stanza:// (e.g. stanza://www.whatever.com/mybook.epub), Safari will automatically open Stanza and download the file assuming Stanza's installed.
Another thing, have you tried using Word to save the .doc file into filtered HTML (in Office 2003, File » Save as Web Page » Web Page, Filtered) and using that to convert via Calibre?
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