Don't take this as anything "absolute", but personally I think the spiritual square is for affecting yourself as in making inner changes, whereas the material square creates outter changes to your situation as a whole. So if you use the spiritual square for health, you may end up cleaning blockages inside of yourself or making other inner changes that increase your health. With the material square, you may affect your overall situation in such a way as to promote better health, like finding a job that has working times which promote a healthier schedule for yourself, or discovering new foods and the like.
Again this is from my personal (and limited) experience with the squares, so make sure you also take into consideration what other members may advise on the matter.