@jackie_w
In the next update, in about half a week, what you want should be rather easy to do (and I'll be happy to explain in depth how, then. Its just that the current version can't really do it too easily). The next update will be html source code based editing/tools, with only the previewer using webkit. But all you would need is a very basic knowledge of html, and obviously you have more than that. Also, in the next update, I don't think it will auto support adding in external stylesheets yet; so you'll just have to add that one line <link type"text/css"...> in yourself.
Anyways the next update will have FAR more features and abilities; including special tools covering a wide range of needs (auto smallcap title, strip certain formattings, uppercase, titlecase, TOC building and saving to epub, etc; all with an easy chooser for making sure it doesn't happen to the wrong things).
@Ortep
Glad there's some inerest! I actually would love to implement an option to automatic conversion, its just that I find it quite hard to work out how to interface with calibre's classes. If someone could provide me with a relatively clear framework of what methods and options are needed, and how to use them, I would be more than happy to add it immeidiatly.