The humanoids from Prometheus are called "Engineers". Unclear at this point if that refers to them creating humans, the Aliens, or both.
Apparently in one of the first Alien movies, there was a scene that had one of the humanoids in full armour in their spaceship "driving chair" that was never addressed. Prometheus was supposed to start filling that hole.
The current plan I think is to have two more movies that bridge to Alien.
Some theories out there is that the Engineers race was split into factions. Some of which colonised planets and were the "science" type guys. Some of the theories for Prometheus is that planet it place on was a military base for the Engineers and the Alien was created as an experiment that had gone horribly wrong. So the humanoid from Prometheus would have been from the military branch of the engineers.
I think the basic premise of Prometheus is the Engineers created us along time ago, and now the Engineers (maybe a different faction) were going to go back to kill us. Maybe the Alien was created to get rid of all the planets an opposing faction seeded.
Tough to say how much the next two movies will clear up what it all means.