Right that worked with the text in my opening statment, but still when I go through the Navigation Bar Links the folders remain in the URL.
Because you haven't edited those links. You have to change all the links.
I feel like giving up, Is this really worth all the hastle I am thinking
In my opinion, it isn't. (But i will still help if you want to do it.)
I really want my site seo friendly
Some people think keywords in the URL are better for SEO.