I couldn't work out the best way to organise the editor for templates and the stylesheets. But when I had done some work on the sub-templates I realised that the best way to build the system was to store css with the areas that use that css. This way if a template is no-longer needed the user can switch off the template and remove it from the system. By doing so it also removes the redundent css.
Clean, quick and just better. ;-)