thesnow:
Basically for example: in the directory tree::includes/templates/classic/css/stylesheet.css , i would also have the original file untouched in the same directory, includes/templates/classic/css/stylesheet_bckup.css
Well, that's going to give you problems right away. Zencart will call in ALL stylesheets with a .css extension, so your site will now load with the stylesheet.css AND its backup, and one will just over-ride the other.
I hope you haven't been doing the same with php files.
As schoolboy says, there are some critical protocols that need to be observed. It is important that you take advice on these issues and don't go off like a bull in a china shop, blindly believing that what you are doing "is OK".
Sorry to sound like a spinster school mistress approaching menopause, but if you carry on down the route you are taking you will spend many hours on the forum in tears later on.