The content was taken from the MapGuide mail list conversation: "Is it possible to maintain a separate viewerfiles for a project‏", by Jackie Ng.

How to:
A virtual directory called /mapguide is created in IIS by the installer. This points to your physical path: C:\Program Files\OSGeo\MapGuide\Web\www

1. Copy this physical path to another directory of yourchoice. eg. C:\Program Files\OSGeo\MapGuide\Web\custom_www.
   
2. Then in IIS create another virtual directory eg: /mapguide_custom.
   
3. Make sure this virtual directory maps to your new physical path above, and has the same IIS settings as the original /mapguide virtual path.
   

Now you can do your required customizations in the copied directory.

To use the original ajax viewer, use your original url: eg. ​http://localhost/mapguide/mapviewerajax/...

To use your customized ajax viewer, change the virtual directory in the url: eg. ​http://localhost/mapguide_custom/mapviewerajax/

Please note that There are relative path references inside many of the *.templ files in the viewerfiles folder & *.aspx located in mapviewnet folder. If you have changed any of these and copy them to another folder as instructed you should change ALL of the relative references to ensure the new folder is using your modified files.