As I understood it (regarding the issue with the two planets):
There are two different planets, A (in Prometheus) and B (in the original Alien).
Planet A was the main hub and base for the development or storage of these biological weapons. On planet A, the base, there were many different ships with lots of weapons. But they (the creators) were all dead here because the creatures, the weapons, had turned against them. They (the creators) could not finish their mission to kill the humans.
On planet B (the one from the original Alien) there was only one crashed ship. These were the same people onboard it (the creators, which inhabited the base on planet A). But these were also killed, by the creatures this time aswell. There was only one ship on planet B - so my guess is that they had left planet A, the base, to go to Earth with the weapons, to try to kill us. But something had back fired and they had to emergency land/crashed on planet B. Maybe this ship had left planet A before everyone there had died, and then were killed while on their way to Earth.
I'll quote myself so you guys can see my post on the new page, I just want to be clear I'm not on the wrong tracks. Is this the general view?