htaccess and multiple applications

[eluser]ontguy[/eluser]
NP. According to the doc, if you're not using mod rewrite $config['index_page'] should have a value.

Another point about the subfolders, you could routing give the URLs the path you have in mind:

$route['admin'] = "backend/user";
http://yourdomain/admin/
would go to
...controllers/backend/user.php

Also what's outline on this page may help to do what you have in mind; http://ellislab.com/codeigniter/user-gui..._apps.html.
It may not though, you'd have to manually switch between applications.