I wanted to come up with a backstory for the engineers which made sense in the context of Prometheus/Alien, and answers the questions that Scott apparently refuses to. I'm sure it's got plot holes, and it's definitely poorly written (just me jotting down thoughts). Anyway, enjoy, or don't. Let me know if you like it, or even if you hate it
Engineer Origin:
The Engineers are an ancient race with technology so advanced as to make them god-like by our standards. They are massively advanced yet possessing of a societal structure similar to a theocracy, with priest like leaders and a caste system.
Their homeworld was decimated by the collapse of its star into a red giant. Having foreseen this, they began the process of colonizing a new planet. Most of their civilization had been relocated to the new world when a disaster nearly wiped out their species. Buried deep in a frozen mountain top of this new planet were the last remnants of a virus which had extinguished the (primitive) life on the planet long ago. It had been preserved in the fossilized remains of one of the creatures to previously inhabit the planet (alien thing from mural). The remains were discovered during the resettling of the new planet and in the process of being examined, the virus spread to the engineer population. The virus was not like anything we would recognize. Instead of simply making the infected sick, it genetically altered them at a rapid pace. This had varied effects from creating mindless zombies to turning them into vegetation. The alterations were wild and unpredictable, but always at a genetic level and always leading to a brutally effective perpetuation of the virus. It spread faster than could be contained.
The planet was immediately quarantined and the remaining engineers were forced to hastily formulate a plan to perpetuate their species. There were less than a thousand remaining.
The survivors collected as much technology as they could from their homeworld and samples of the virus from the dead world and began to experiment with the virus on LV422. This facility was explicitly created as a R&D lab to study the genetic effects of the xeno-virus. The engineers had success. They were able to isolate and synthesize the millions of nano structures which allowed the virus to attack the DNA of living things. The effects could be manipulated for a desired outcome.
It was at this time that the original derelict from Alien crashed. This ship was transporting newly discovered egg samples from the virus world. The pilot was infected by a face hugger during the recovery of the eggs, but awoke apparently (to him) unfazed. He set course for LV422 but just prior to arrival the xenomorph began to stir. He was able to quickly re-route the ship to crash on a nearby moon (LV426) and set off a warning beacon prior to the xenomorph bursting from his chest and killing him. The extreme g forces created in the impact with LV426 crushed the young xenomorph just after it hatched, which created the acid burn hole in the floor. The other engineers, being able to immediately interpret the warning beacon, knew to leave derelict where it was.
The engineers learned from their near extinction that unknown alien threats can not be predicted, and they are unlikely to survive another ordeal similar to the outbreak of the xeno-virus. They learned not to keep all of their eggs in one basket...so to speak. The Engineers solution was to repopulate the galaxy with their own DNA so as to rebuild their dying race. By seeding as many worlds as possible, they hoped to flush out any threats while simultaneously recreating their population. In order to accomplish this, they developed a variant of the xeno-virus which would destabilize the DNA of the infected and cause it to spread out and bind to any organic material nearby. Thus began the process of seeding the galaxy. After identifying a habitable world, The Elder engineers would choose a sacrificial recipient and he would become the seed of life on that planet. This process was repeated dozens of times.
The surviving engineers, after seeding a new planet, would assign "watchers" to that planet. These watchers would place themselves into hyper sleep for a long time, a few hundred years. Upon waking they would "check in" on the planets they had seeded. They would introduce themselves as Gods and begin teaching the inhabitants how to live. They would pass along small bits of technology to help their children along the way, but not so much as to upset their natural evolution. They would give them fire, or show them how to cultivate crops. Being vain creatures they would also demand worship from their children, as they viewed them as a half-breed not yet worthy to stand side by side with their creator. This is where the cave paintings and sculptures Holloway and Shaw found came from. The engineer "gods" would tell their children that when the time was right they would join the gods amongst the stars. The "starmap" wasn't specifically pointing to the research facility as an invitation, but rather to say "you came from here, we made you, and when we are ready, you will join us". It was never "come here and check out our lab". They had never intended for these populations to develop space travel without the engineers "holding their hand".
From time to time the engineers would awake to find one of their seeded planets had abandoned their guidance and fallen into primitive violent ways. The engineers deemed such planets to be a threat to the rest and needing to be annihilated before their technological advancement gave them interstellar travel where they could spoil the rest of the seed worlds. In order to accomplish this, they again turned to the xeno-virus except the desired outcome was destruction instead of creation. They managed to synthesize what we know as the "black goo" or "the pathogen". This genetic bioweapon bonds to the host DNA and alters it at a rapid pace. Depending on the infection site and host genetics, it may either change the host into a ravenous violent monster, or ravenous beast will be created from the raw genetic material of the host, killing it in the process. The beasts created are primitive forms of what we recognize as the Xenomorph. The engineers developed this weapon as a failsafe to keep rogue civilizations from threatening their empire in making. Once a rogue planet was identified, the pathogen would be manufactured, the fleet of juggernauts would be armed, and the mission to exterminate would be launched. Upon completion the planet was quarantined and a new seed world would be identified and seeded. 
This process is what was taking place with earth. The watchers were making their galactic "checkup rounds" and discovered earth circa 50 BC - 100AD (exact date unknown). The Roman empire is running around conquering everything, inventing the drunken orgy, worshipping false gods, and generally misbehaving. They deem our civilization as too violent to continue and decide we must be eliminated. They begin manufacturing the pathogen, except this time there was an accident. Somehow, the pathogen breached containment and infected one of the engineers. This is what has happened in the holograms we see in Prometheus. They are suited up to protect themselves from the pathogen, but one of them is infected. The pathogen is mutating him and the others are fleeing, for they know if it infects them, it will be their end, and furthermore that the rogue civilization on earth could continue to develop unchecked, and eventually threaten the rest of the galaxy. They are desperate to contain the outbreak but they have crafted their weapon too well. It spreads rapidly and kills them all, but one. The last engineer was in the process of being prepped for hyper sleep when the outbreak occurred. He was sealed in by the other engineers in the hopes that another group of Watchers would find him before the rogue civilization on earth could develop space travel.
***Cue Prometheus*
Details
The "suits" the engineers wore are actually bio-engineered enhancements which allow them to interact with their technology using a synthetic form of telepathy. It enhances their strength, and nourishes their bodies by absorbing nutrients from the environment and energy from the sun. It is an all purpose bio enhancement based on the technology derived from the xeno-virus. It is a permanent accessory to the engineer.
The larger suits, what we recognize as the space jockey, are the engineer equivalent of a hazmat suit combined with a space suit. Full atmospheric processing, radiation shielding for deep space travel, comprehensive bio infection shielding, and integrated hyper sleep capabilities. The bio suit is designed to accompany the bio-enhancements the engineers donned. They are symbiotic with one another.
The pilot chair is large and odd shaped for a specific reason: Once the engineers bio-suit has encased him, the Pilot's chair acts as a conduit through which the engineer controls the juggernaut ship. The chair allows the pilot to control the ship as if it were his own body. The large "cannon" structure is a huge focusing antenna which synchronizes the engineer's mind to the ship's AI and facilitates the transfer of information from the ship to the Engineer, and control from the Engineer to the ship.
** this will be shown to be why the derelict on LV426 crashed...it's pilot was infected by a xenomorph. When it burst out of him it caused the ship to crash because the two were linked telepathically. **
