Installation/configuration problem

[eluser]Unknown[/eluser]
I'm trying to install CodeIgniter 2.0 in a similar way i was using it with CI 1.6
I want this directory structure:

Code:

- .htaccess (redirect everything to webroot)
- application
- system
- webroot
   - .htaccess
   - css
   - js
   - images
   - index.php

I'm using .htaccess to redirect the whole thing to webroot/ and thereafter i check through another .htaccess if the requested URL exist in the webroot/ directory. If exist, output the file, else redirect to index.php which is CI index.php file.

I've dig into CI Router and problem seems to be related to URI retrieved from the server.
In my case, my project is in /Sites/DemoProject/ and URI parsed by CI Router always start by /Sites/DemoProject/ which is my base url.

Is this a bug or something i'm doing wrong?
Thanks