Yep. Worked just as you said. After laying out the UV's in Maya and painting a rough skin I opened the model up in 3dGS modeler. Next I selected a cluster of faces (which corresponded to the texture grouping in Maya for each skin. Then opened up the "skin manager" and (with the faces still selected), selected the skin and hit the "set skin" button.

All done.

I haven't noticed a hit in framerate but then again, I'm not using any kind of official tools to measure it.

Thanks again,
Todd