[eluser]chobo[/eluser]
I searched around and came up with a pretty decent solution, to save others time I'll post it. I split my application folder into two sites, one is the main one everyone sees, the other is the admin/cms site, they both share the same system folder. I then made a new folder in my webroot (where the index.php front controller is) and made a copy of the index.php and threw it in there, I also had to make another copy of my paths file and gave it a different name, it was just to specify the application path. I then added a .htaccess to that folder banning everyone but me, so there you have it