One thing: If you don't want everybody to see the "menu" for diabling/enabling sef, do NOT enable the plugin from the plugin list, but got into the Edit Plugin screen and select Yes, then save.
One thing that should/could be made better is the error handling that you have to disable in the Joomla Config, if not you might have to wait a long time before you understand that it broke somewhere because of a php error/warning.
Great tool, needs some HTML makeup though :-) but I can live without that because the backups are good.
You can either patch you joomla files by hand as is clearly indicated, OR you can use the provided patched (different download) files and overwrite the ones on your server. After that you simply have to select the kind of protection you want. Here a dropdown or similar would have been welcome, but nothing serious here.
Securing your website like this is a breeze! Thanks Walter!