No, you will only increase the magic skill your primary effect (which is the first one) is based in.
So if you have a spell that provides a light spell as its first effect (Illusion) and a restore health effect as its second effect (restoration), you will only gain skill in Illusion when you cast the spell. The light effect is the first effect in the list, and that is the effect that determines which school the spell will be based in, and therefore which skill will be increased when you cast it.