The problem you're going to have here is actually exporting that 2nd uv channel, as most formats do not support it. When i was trying to get a 2nd uv channel from modo to maya, to export into game i had to do some retarded stuff. What i ended up doing was saving out a 2nd copy of the mesh with the LM uvs and loading that in with my regular mesh, creating a new uv set on the regular mesh, and then doing "transfer attributes" or something to copy the uvs from one to the other based on vertex positions, was a bit of a pain to do, but it worked.
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Edit:
Also be sure that the Vertex Map Type is set to UV Map on the popup that comes up.