[eluser]neen[/eluser]
You can override config settings:
$this->config->set_item('config_var', 'value');
I am using this to use a local.php config file in config/ and then I concat the vars in there into another config variable
In this way I can have a config file that gets edited locally (that's not under version control) so I can set the (relative) paths to the CI URL
$this->config->set_item('common_url', $this->config->item('base_url') . $this->config->item('common_path'));
// set the new base url (add local path and site path if needed)
$this->config->set_item('base_url', $this->config->item('base_url') . $this->config->item('site_path'));