Don't flame me if I'm wornge, but I think the way that halo displays its models and textures is completely different from the way that a 3D editor displays models and textures. Again this is a guess so dont flame me if im wronge.
In order to make a new skin show up you have to open any map in HMT, got the [bitm] tag, click the skin you want to overwrite, click on the side Inject texture and find your new texture.
