Thanks for your quick reply.
If I understand you correctly, if it says in the theme .info file:
; Add theme CSS files
stylesheets[all] = css/base.css
stylesheets[all] = css/layout.css
You would just put the name of the class there. You would define the class in the css files for your theme.
You can define the class anywhere, just make sure that whichever file you use is loaded...