Multiple Apps (CodeExtinguisher) - shoot me now!

[eluser]m4rw3r[/eluser]
The index.php files link to both the system dir and the application dir (which depends on which application you want to use).

So the index.php should link with basepath to your system dir, and with apppath it should link to your main app.
The backend.php file should link with basepath to the same system dir, but with apppath to the CE app dir.