Multiple Apps (CodeExtinguisher) - shoot me now!

[eluser]ywftdg[/eluser]
ahh ok the root index.php, backend.php files all makes sense now.My only issue now is how is this CodeExtinguisher actually placed into this sub folder 'application/admin/'

It seems it has its own system folder, etc etc, all of the items I am assuming I don't need since they are already in my root? Sorry, new to all this fancy footwork stuff...