The stylesheet in the Site Settings is used to override skin styles.  However, I would never suggest you use it.  Additionally, a skin developer should never rely on that.

I believe that the color option in the Module Settings is simply for the background color of the module.  Again, I would suggest that you not worry about it.  The only things in DNN that you should worry about when creating your skin, is overriding the existing styles in the default.css (_default directory), and clearly defining your own CSS heirarchy.