SPOILER WARNING!
Rich, you got the planets' numbers mixed up, but otherwise you're right. In Alien they find a derelict spacecraft on LV426 that's likely been there for thousands of years since the remains of the pilot had petrified. The planet in Prometheus is LV223 and likely the point of origin of the alien spacecraft in Alien, on its way to somewhere (possibly Earth?) with a shipload of bio weapons (aliens) when something went wrong. In Prometheus they reanimate an "Engineer" that has been in stasis for thousands of years. What I got from the opening plot was that perhaps some sect or faction of the "Engineers" seeded Earth (and who knows how many other worlds) with their DNA, thus creating the very first life here. That means the "Engineers" must have been around for at least 3.8 billion years. For some reason another faction (or the same guys just changed their minds) is trying to undo what they did.
Another theory I have is that LV223 actually used to be an inhabited planet of the "Engineers" (or at least one of their worlds), a welcome site so to speak, and that another of their "child species" followed their cave drawing instructions and came to visit. A conflict ensued that destroyed the "Engineers" at LV223 and they've decided all their "children" are threats and must be wiped out.
Anyways, it's a good film with many unanswered questions. I'm looking forward to any sequel Scott decides to make.
Edit: It's LV223...