Here the normal map was created in ZBrush using ZMapper from the model's sculpt below (shown in level 7 on left; level 1 on right - Fig.08).
Now the problem is this: when I apply the maps to the model in Maya, both maps are going to apply to the "Map1" UV set, even though I want the colour texture to apply to the "Half" UV set (Fig.09 - 10).
To fix this, I'm going to use the UV-Centric, UV Linking, Relationship Editor (Fig.11).
This will allow you (with your model selected) to choose which maps go to which UV set. In the following two images you can see that I have re-linked Map1 to work with file2 (my normal map) and Half to work with file1 (my colour map). Notice how this fixes the colour texture's appearance on the mesh (Fig.12 - 13).
When I turn on the High Quality Render, my normal map applies to the whole surface UV set where as my colour map applies to just the half UV set (Fig.14)!
Using the Relationship Editor for Layered Textures
A third usage of UV sets can been seen when we try to create tiling textures. In this demo I have a flat plane simulating a wall, a colour map of tiles, a matching bump map, and a graffiti pattern to be placed over them. They are hooked up via a Layered Texture node in the hypershade with the graffiti on top set to "multiply" (Fig.15 - 16).