You want to make a copy of your wow folder.
Specifically, you do not want to include your Cache or Data folders.
Some people exclude their Interface folder as well, but if you'd like each folder to have different options then you'll not want to do this.

Then we create a symbolic link from the main/original wow folder to each of the copies.
Specifically a symbolic link from the folders which we did not copy.
So that the new folders will have identical folders to the original.

There is a command line thing to create symbolic links, but I think this program is easier.
It requires you to download files from microsoft's site in addition to the version of the program for your operating system.
The program is here: http://schinagl.priv.at/nt/hardlinks...kshellext.html

On patch day, you'll want to break the symbolic links.
Patch the parent/original wow folder.
Then remake the symbolic links.
Then copy the wow.exe file from the patched folder and paste into each of the copies.