You can either make your own skeleton, or find the ms3d file in your milkshape folder that contains the stock TGE skeleton.
Be sure to assign the vertexes to the corresponding joints and don't replace the .dsq files (Unless that is your intention)
Groups are not needed for each joint or node as I am assuming but are need for separate textures.
.dsq sequences are just sections of the animation in the .ms3d made readable for torque in chunks.