I've been trying to figure this out as well.....It doesn't seem to do anything automatically like the new update said it would.
I did the same thing, had a second skin in MED that should have worked, saved the model, brought it into MED and ran my level, and saw no difference, no lightmap being used even though I have one applied as the second skin in the .mdl file. It looks like it's just not doing anything automatically with the second skin like it says it should on the beta page.....
Do we have to add some code to get it to actually use the lightmap?