Documentation
CodeIgniterAuthenticator.logged_in_key
This enables you to specify the session key to look for when authenticating the user with CodeIgniter PHP. This option defaults to "isloggedin"
$moxieManagerConfig['CodeIgniterAuthenticator.logged_in_key'] = "MyLoggedInKey";
You can then use this code to authenticate the user:
// Login the user and override the filesystem.rootpath setting in your controller
$this->session->set_userdata('MyLoggedInKey', "true");
$this->session->set_userdata('moxiemanager.filesystem.rootpath', "/var/www/myroot");