CI in a Linux environment setup

>>> Could you elaborate on that? in my project/system directory there are few folders I don't know where to specify what you say.

index.php -> $system_path = 'system';


I have $system set to: 
   $system = '/var/www/ci2/CodeIgniter-3.1.11/system';

I also have the previous version:  
  $system = '/var/www/ci2/CodeIgniter-3.1.10/system';

This is because it is easier to share one version between other projects.