If you are referring to my Fortress level I must say that order of images in AUM is actually reversed I first create geometry in WED, export it to MED & then do lightmaping in Blender.

You can check this baking tutorial for simple info on process:

http://vimeo.com/2745768

I'm not sure what you mean when you say lightmaps in fbx format but, if your modeling in Blender & not WED or MED, you can export your textured & lightmaped model in two separate fbx files, re-save them as mdl's & import second model uv mapping & texture in first model. Second & much easier option would be to use Ventilator's plug-in & save directly to mdl

As for me, I do atlas mapping on second skin set in MED & export that to Blender. Then after lighmaping in Blender is done I just save image in tga, re-format to dds & make a swap.