You have to be more specific that one can help you.
Which version do you use?
What sort of effect does it have?
How looks the mesh in the Skin Editor?
etc.
I use it quite often, and it is great to create a shadow map with ventilator's tool.
If you use it for a skin that want paint in photoshop or something similar, then it makes only sense when you select certain parts, which should be collected, click atlas mapping, and scale and move it on the skin.
Do you set a new skin before you map?