multi controller in subfolder

[eluser]CroNiX[/eluser]
/application/controller/backend/controller1.php (you can only go 1 directory deep in /controller, so you can't have /controller/dir1/dir2/controller1.php)

URL: http://yoursite.com/index.php/backend/controller1 (assuming you haven't removed the index.php using htaccess)

Personally, I'd just have "backend" and leave the front facing controllers in /application/controllers. Otherwise your urls for the frontend will all have "frontend" in them unless you remove them with routes.