I stumbled across how to add multiple themes for the Directory Plugin. This example clones the default Directory theme, allowing you to customize the new theme to your heart's content. It's quite fun, so follow along:
1. Go to wp-content/plugins/directory/themes directory
2. Copy/paste the default folder (because "default" is the theme folder)
3. Rename the default copy to newtheme and edit it's style.css
4. Change the first line, Theme Name: Directory Theme to Theme Name: Directory My Theme (save)
5. Go to your WP Network Admin --> Sites --> Your Site --> Edit, click on the Themes tab and enable Directory My Theme
Now, when you go to your sites admin panel (the site you have your directory on), it will look like the screen shot attached to this post.
The Directory plugin is quite robust. There are lots of cool things you can do with it. Best of all, you can customize it, just like any other theme.