Configuration
Edit /path/to/yoursite/js/fckeditor/editor/filemanager/browser/default/connectors/php/config.php and add the line:
$Config['UserFilesPath'] = '/userfiles/';
..where /userfiles/ is the path to the directory to be used in the file manager, relative to the DocumentRoot.
Edit /path/to/yoursite/js/fckeditor/fckconfig.js and add/uncomment the following lines to use the PHP connectors:
FCKConfig.LinkBrowserURL = ... + '...connectors/php/connector.php';
FCKConfig.ImageBrowserURL = ... + '...connectors/php/connector.php';
Also edit any other configuration variables in this file to suite your setup if you need to.