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I've never done this but I have a feeling it relates to sets.
Its in Maya help under "Bake-sets" I've just had a wee gander through the menus and thats all I can see that might help
I'm not sure if I'm totally understanding the problem but can you not just lay out the second set of UVS in right next to the 0-1 space and then just slide those UVs into the default 0-1 uvspace for when you are baking and move the original set out?
If you use Move Component it assigns a history node to the movement so you can slide the uvs sets exactly 1 unit and back again, thats how I've dealt with multiple uv sets before
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