Basically, you select the materials that will not be on a given map, and use "" to turn them off. Map what's there, and save the texture map, with "Ignore hidden facets" checked. Then select the visible material, and the materials that will be visible on the next map, and use "" to toggle the visible facets invisible, and the invisible ones visible (it only operates on selected facets), then repeat the save proccess.

Remember, kids! Napalm is Nature's Toothpaste!