This applies to Ubuntu 12.10 (may work with older versions)

First you will need to check that Apache is really using /var/www as the website root:

$ grep DocumentRoot /etc/apache2/sites-enabled/000-default

DocumentRoot <path/to/apache/root_dir>

If the path stated in the output is different, you should change that in PHPStorm.

Also you may not be able to place your php files there because the permissions on that folder. To solve this, jst change the permission of /var/www (or the correct path) to your current user:

sudo chown -R <user>:<user> /var/www

where <user> is your username.