I'm sorry. I didn't read your original post very carefully.
BenRule myRule = new BenRule("No replying to email before finishing the first cup of coffee.");
Ben.rules.add(myRule);
Changes to the style sheets will get you as far as modifications to color schemes, background images, and fonts. You won't be able to do layout changes, which is the part I missed when I originally read your post.
But, there are ways to accomplish layout changes, by which I assume you mean things such as:
o Moving the menu from the top to the left side bar
o Moving the search box to another part of the page
o Adding a footer
o In general, moving things from one part of the page to another
You can create what are called custom site definition templates, and modify the backend .aspx pages in the templates. There are a number of blogs out there on how to do it. Here is one: weblogs.asp.net/.../108396.aspx.
Keep in mind the best practice of not editing the files in any of the default SPSXXX directories. Make copies of the original folders, and make your changes there. Then follow the steps in the blog to register the new site definition templates in the XML files.