All of your changes should be saved, because those options are stored in the database. However, it is always good practice to save your settings before you make any major changes by going to Montezuma Options > Export Import > Export Settings and saving the contents of the Current Montezuma Settings field to a text file. If anything seriously goes wrong with your modifications, you can always return to a backup.
Good luck with your changes; once you get it working, I'd be interested to see how you implemented it, so please share a link to your site when you're done.