Hard to say without seeing your current code.. I just suggest having a stylesheet control in your masterpage that prints different css tags for different skins..
are you using a masterstyle sheet with @imports to several sub stylesheets? (I use that way). If so you can easily combine stylesheets for different templates.. like have a general positioning stylesheet but different typografy stylesheets for different skins..
Then you can store skin information in in a cookie or something fr wich skin you use or so I assume.