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MadFish:
You're correct about this. This particular theme has a very lean style sheet, and has a lot of settings hardcoded in theme.html. In particular, the background color of the left and right columns is defined in lines 39 and 120.
The same is true about the table holding the logo and the banner. Has its bgcolor defined in the theme.html file, line 26.
To ease the maintenance work in this theme, it might be a good idea to follow sunsnapper's advice and give these TDs a specific name, as occurs in the default theme. This way, to change the appearance of the theme you'd edit the style file, not the HTML file.
Cheers.