Jason,
An option would be to create 3 of the same skin layouts with different names, say mo-skin, uat-skin and prod-skin, and then also create their respective CSS files mo-skin.css, uat-skin.css and prod-skin.css which will be loaded last in the stack of skin related CSS files. Within each of the individual css files you can now specify the different settings and these will over-ride the default settings of the skin.css file.
Example css in skin.css file making the background color white:
body#body{
background-color:#fff;
}
example CSS in mo-skin.css making the background blue:
body#body{
background-color:#00f;
}
the same CSS in uat-skin.css making it red:
body#body{
background-color:#f00;
}
You can then use the appropriate skin as the default for each setup and your changes will apply.
Hope this helps.
Rick.