Found the location. \Program Files\Common Files\Blizzard Entertainment\World of Warcraft Installer

[s]I guess I can just use the installer for each wow copy. Should have researched a bit more before posting![/s]

Okay, it is not as easy as running the installer because you can't choose a path. This is easy to work around, however.

Open up your registry editor (command is REGEDIT) and navigate to:

HKEY_LOCAL_MACHINE\SOFTWARE\Blizzard Entertainment\World of Warcraft

Here you will see two keys that need to be changed to reflect the directory you want to update. (please note double \\ exists here but when you edit the key it will show a single '\' so don't add double.

"GamePath"="c:\\WowWow5\\Launcher.exe"
"InstallPath"="c:\\WowWow5\\"

After you run the installer and want to run it on another directory just change it with the registry editor. No need to reboot or anything like that. Once updated rinse and repeat for all your wow folders. The update doesn't take that long once it has been downloaded. Pretty quick!