Dear Steve.
I guess that's why I don't like to use CMSes. I like to have more control over layout and such, and I find I spend less time doing my own CSS and HTML than I would trying to get my CSS to work within the CMS CSS. The more customizing you do with the CMS, the more problems you potentially have when you do upgrades in the future.
Like I said though, it all depends on how many pages you're maintaining. At some point, it's better to just work within the bounds of the CMS and give up some of the customizability, in order to have better maintainability.
Please don't worry to much about theming. CSS Stylesheet is already there and will be ported to themes if necessary.
Greets Marcus