Lawrence Lee at Radio Userland posted an excellent tip in Userland's forums today, in response to Lisa's question about customizing the #template.txt file differently for her weblog and her Desktop Website:
How do I customize the appearance of pages in the Desktop Website?
You can customize the desktop website home page by editing the template from the preferences page. But you can also change the appearance of the news, preferences and other desktop website pages by placing a #template.txt in the /www/system/ folder.
Note: This won't be applied to the Folder view pages on the desktop website.