The best bet is to make the uv-map in blender.
Nonetheless, it is work, and there is no automated way to do it in a satisfying way.
Atlasmapping is only good for a shadowmapping.
When using MED for the layout, you should use the 6sided method.
For this you should select the faces of the model like you did in the second pic, layout it, then select the next reasonable connection of faces, layout them, etc..