So it seems to me that there are two possible interpretations of the information we have.
1. The Engineers created xenomorphs as a weapon, and created the black liquid as another weapon. Somehow, the two are related enough that there's a xenomorph mural in the urn room, and related enough for a series of black liquid contamination events to ultimately produce something like the Deacon.
2. The Engineers found the xenomorphs, whose unique and essentially impossible biology became the foundation for the Engineers' technology ("new alloys, new vaccines," to echo Gediman). Their ability to borrow the genetic characteristics of their hosts became the basis for the Engineers' black liquid, which manipulates DNA and which can apparently transfer Engineer DNA to lower lifeforms. Their structural biology became the basis for Engineer architecture and shipbuilding, explaining the Gigeresque designs of Engineer construction. The mural in the urn room was an expression of reverence for the creature which gave them their technology, and the Deacon was either a product of the re-emergence of xenomorph traits following serial black liquid contamination events, or a product of xenomorph DNA in the "weaponized" black oil on LV-223, as opposed to the terraforming/species building black oil used in the opening sequence.
Personally, I prefer the second option. As others have mentioned, it makes the xenomorph seem much more eldritch - it predates the Engineers, who are already billions of years old, and it is a product of the cold, unfeeling processes of the universe itself rather than a product of mere tinkering. It also gives a bit more meaning to the title of the latest film. The titan Prometheus gave man fire, which is both incredibly useful and incredibly destructive. Hypothesis 2 would have the Engineers finding the xenomorph an incredibly useful gift from the cosmos, but the Jockey on LV-426 would have found it incredibly destructive as well (and at least until the next film comes out, I like to imagine that the entire species learned the same thing).