This graphical Prometheus species origin chart probably will not clear up any of the problems you did or did not have with the Alien sort-of-prequel's logistics/science/forced-drama, but it does function as a pretty good reminder of exactly what I'm prettttty sure writers Jon Spaihts and Damon Lindelof were asking us to swallow regarding the film's genetic combinations. The only thing I might add is that Guy Pearce + Makeup & CGI = Inexplicably-Expensive Way To Make an Old Guy. (Spoilers below, of course.)
The last one should maybe be "alien xenomorph + hilarious wind-up chatter teeth," but yeah, that's pretty much right. I think.