So after giving it too much thought, this is how I have come to think of it.

Initially the Engineers used the black liquid to terraform planets, going to planets with little to no life and using just a minor amount of this accelerant to bring forth a biosphere.

But perhaps on many of these worlds a strange pattern emerged, the creatures we call Xenomorphs would repeatedly evolve and emerge as the dominant lifeform on the planet.

(fitting with the predators theory of convergent evolution)

This seeming miracle would lead to groups of engineers coming to worship the Xenomorph, and thus provoking a civil war that tore the engineer society apart.

Some Engineers fought so long in these wars they became fused into their bio suits. Eventually the Engineers numbers dwindled and they largely disappeared from the universe.

The ship found in prometheus was a ship of the hostile Xenomorph worshiping faction, they intended to bomb the earth with the black fluid because in their minds humans are an abomination, a creation of their ancestral enemies.

The Xenomorphs themselves secrete a version of the black liquid that humans call "royal jelly" though it is unrefined and far less pervasive and invasive with its effects.

PErhaps their ability to generate this liquid, a liquid that the Engineers probably spent thousands of years developing, a liquid that gave themselves the delusion that they were gods... is why so many of the Engineers began to worship them.

From a behind the scenes perspective its amazing how often the Xenomorphs would be associated with transformative liquids, mutations, and other stuff that would later become a major factor of the movie Prometheus. And it makes it hard for me to believe that there wasnt influence from the comics and books towards the film.

Simimliarly the Space Jockeys are often associated with Terraforming, and are contradictorily portrayed as both benevolent and malevolent just as they are in the film.