Everything explained! (spoilers-inside)

I just watched this awesome film and was confused about a few things, then suddendly it all made sense; in my explanations I call the engineers the pre-humans: - The pre-humans are under control of the aliens, and in fact the pre-humans may have been created by the aliens.  The aliens need the pre-humans to gestate which is why they don't just kill them outright; the aliens use the pre-humans to mother their young.  It's no coincidence that the alien at the end kills the pre-human by injecting part of itself into the pre-human through the pre-human's mouth - just like the alien did in the first part of the film with the human (biologist guy wearing glasses) and indeed to John Hurt's character in the first alien film.   All of this shows that the aliens breed or at least use humans/pre-humans as incubators for their young.  This is the key key point. Unfortunately the gestation results in death for the carrier, so the aliens need a fresh supply of humans. - The aliens (not the pre-humans) are in control, they are the ones who seed life throughout the galaxy using the pre-humans.  What kind of life?  Well, they need human life to sustain their own, so that's what they seed.  At the beginning of the film we see a pre-human who has been dropped off onto Earth with his task ahead of him - he has to disperse his DNA thoughout the Earth to seed life, specifically human life. He does this by drinking that wierd black stuff (the same stuff that David slipped in the doctor's drink?) -  The archaeologists uncover the same star-pattern all over the world from ancient races and comment 'it's as if they wanted us to find them'.  This part is not explained, i.e. how all these images ended up all over the world, i.e. how all these ancient races received these images, but perhaps Earth was visited by the pre-humans when human life evolved.  Anyway, the message is clear - the aliens (and their slave pre-humans), definitely DID want the Earth humans to find them. - When the humans (after millions of years of evolution) travel across space and enter the control room of the alien spaceship and wake up the pre-human, then guess what?  That's a signal that human life on earth has evolved to the point that it could then sustain alien life. In other words Earth is now ripe - brimming with billions of humans who can now be incubators for the aliens. The control panel lights up and the 3-d starmap shows Earth in red - Earth is now the next destination for the alien's progress. - David is asked by one of the crew what the place is they are entering and he says "It's a cargo hold".   We are also told and see that there are thousands of pods.  From previous frames in the film, it seems to suggest that the pods are full of little worm like creatures whose intermediate stage is the white thing in the black soup that got the biologist guy wearing glasses.  If the pods are full of worms then that's probably enough to take over the whole of Earth. - David says 'in order to create life you must destroy it first'. This simply means that most of human life on Earth is now going to perish when the aliens get there and colonise it, i.e. the aliens will flourish and multipy, the humans will die.  The alien's plan is to use most of the population as incubators and subjugate the remainder for the next stages. The confusion in the film, stems from the fact that the captain thinks that the pre-humans created the aliens as some kind of weapon or biological experiment.   If you turn this around, i.e. aliens creating pre-humans, it all makes sense.