Yes, the content margins for the More Programs menu do work. Just to be certain that I give you accurate information, it might help if you were to explain what it is you are trying to accomplish. I'm not trying to be difficult, but frequently mistakes are made when trying to help someone because of terminology. Are you referring to the More Programs Panel background or to the More Programs Menu background, both of which have control margins. If you could just give us a better idea of what you are trying to do, e.g. shift icons or text left/right, align the menu highlight item, etc, it will be easier to help you. A screenshot of the problem also helps a great deal in most cases.
As to a guide for Skinstudio, there is no aftermarket commercial guide available, but you can find Stardocks user guides and a video demonstration here: https://www.stardock.com/products/skinstudio/docs.asp
Hope this helps you, and I'll be waiting for your response.