Ok, the custom CSS box and keeping it in the uploads directory works great. I'm encountering an issue with multisites.
You cannot customize it on a per site basis. It will affect every site that is using the plugin. Right now, because I bought the PRO version, I'm just using the PRO version on the one site that needs it.
The suggestion here is to use the same method as I suggested before in the PRO comments. putting a check box that bypasses the plugin CSS and instead uses the theme CSS would be a good way to go about it.
Thanks and great job!