Using Subdomains for multiple apps

Has anyone setup or know how you would setup your folders to share 1 codeigniter install for multiple apps using subdomains. Lets say I want to use site1.domain.com and site2.domain.com as my public folders which contain the index.php files.

site1.domain.com
   -index.php
site2.domain.com
  -index.php

where should the app, writable and testable folders sit?
Where should the system folder sit?

Any suggestions?