Prometheus Ending

I loved the movie, but I am confused about the ending. The “Space Jockey” (Engineer) is the film is supposed to be the last living one, and the ship that crash landed at the end of film is the ship that Ripley finds in the movie Alien. Right? However, at the end of Prometheus the Engineer is not resting on the navigational chamber, because, according to Prometheus, the last Engineer died elsewhere—where he gives birth to a Queen Alien (who later nests a bunch of eggs). Who is the Space Jockey who died and had a hole in the middle of his chest in the first Alien movie? Was it another ship, or this ship they find?