Spent most the day trying to figure out this problem. The closest thing I was able to find, was a comment on one of the Yii Framwork forum posts. For now, I'm running Boilerplate with subdomains like they recommend in this comment.
http://www.yiiframework.com/wiki/155/the-directory-structure-of-the-yii-project-site/#c9444
I'm not sure if this is the correct way. But it works.