Note that CMS_SETUP provides locations set by default or from configuration file. Now theme related resources can be found under site/modules/$mod_name/... or site/themes/$theme/modules/... so only theme related resources can be overriden for now.
Examples CMS: examples
api: API is a simple example showing how to build a custom CMS using EWF. roc_api: api build using a CMS library using modules, themes, etc.