Multiple Apps (CodeExtinguisher) - shoot me now!

[eluser]ywftdg[/eluser]
Ugh, still in a haze here. Ok, yes I have my two files on root, index.php and backend.php. The index is working pointing to the application/client area as my main. The code extinguisher still wont load. As I mentioned above, CE comes with its own system, yada yada, so I pointed to what seems the actual application area: application/admin/system/application/backend

But no load. Any you guys ever run this app and i so where did you put it and how was it targeted? I even tryed moving just the 'backend' folder up into my application folder on root, bypassing CE prepackaged system and such, still no load targeting just application/backend