How do you disable the built in color schemer ?

Yes sure, just deleted the color folder and remove the following code from template.php:

function _phptemplate_variables($hook, $vars) {
  if ($hook == 'page') {

    // Hook into color.module
    if (module_exists('color')) {
      _color_page_alter($vars);
    }
    return $vars;
  }
  return array();
}

And the multiple style.css files are from different directories. The color module adds one, and the fluid version adds another.