DNN sites have the following order of precedence for Style sheets (CSS):
1. Skin.css
2. Portal.css
3. Module.css
Where skin.css has the highest precedence and module.css has the lowest precedence. This means that if you have the same class, for example a DIV class defined in skin.css and module.css the DIV class in the skin.css will override the DIV class in the module.css.
If you are running multiple portals/carts in the same portal and want to style each cart differently with different colors, etc. then all you need to do is copy all the styles from the module.css to your portal.css or skin.css and change your styles to the ones you want.
After you copy the styles they will exist in both the skin.css and module.css. The styles in portal.css or skin.css will override the styles in the module.css and since the portal.css/skin.css files are per portal it will give you the ability to style the cart per portal.