For instance if I am going in a heavy lighting damage area do I get more protection wearing all lightning resist gear? Or is a single item that has say level 3 lightning resistance the same?

I don't know for sure, so I'm always trying to use different enchants. There are different wear for armor, which points to hitzones. Maybe armor defend only covered zone? Just now in a battle against Soul Keeper in Catacombs, I was able to sustain longer under his lightning with robe and helm in comparison to only helm with lvl1 lightning resist.

Magic and enchants do stack though. Haste boots 1lvl gives 3 speed, while magic level 11 gives additional 30 speed, in total 33.