OK, I am a bit confused. Below is a copy of the Override System that I have.

Code:
The Override System -   Wherever you see a folder named "classic" you can safely add your own /CUSTOM folder.
 
includes
    languages
        classic
        CUSTOM
         english
             classic
            CUSTOM
            extra_definitions
                classic
                CUSTOM
            html_includes
                classic
                CUSTOM
            images
            modules
                order_total
                    classic
                    CUSTOM
                payment
                    classic
                    CUSTOM
                shipping
                    classic
                    CUSTOM
    modules
        classic
        CUSTOM
         debug_blocks
         order_total
         pages
         payment
         shipping
         sideboxes
             classic
            CUSTOM
    templates
        classic
        CUSTOM
        template_default
 
Replace CUSTOM with your own folder name.
I must be reading the graph incorrectly. Is everyone saying that pages can not be replaced under CUSTOM?

Sawhorse