My reasonings linking the two timelines and attempting my own explanation.

OK so here is how I think the two films could link in the "Alien Universe" Let's sort the idiots out first. This film is not set on LV 426 and the Derelict in Alien is not the one you see crashing in Prometheus. OK Imagine this story I think it could hold water. Regarding the Space Jockey in the Film Alien. Hundreds of thousands of years ago a hapless bunch of space jockeys or a single space jockey find the Alien eggs on LV 426 as written in the Alan Dean Foster Novelisation of Alien... one gets infected and managed to send a distress signal before he violently dies in his seat... but basically the derelict didn't crash it was just there investigating as space travellers would. So MAYBE that happened or maybe they already had the egg etc and some queen erupted from the Sj and seeded the eggs under the ship which ever canon works for you but the important point is this is ANCIENT history even for the Sj. This explains why the Nostromo Crew found it fossilised and out grown in its seat and the Xenomorph Alien life form was perhaps closer to it's Original form than we encounter in Prometheus. So then a bunch of Other Sj come across this derelict, as they perfectly understand the warning and perhaps go to find out WTF happened. They then kill the queen which Layed all the eggs so this explains that they have encountered the Xenomorph and as such explains why it's explicitly depicted in the Mural in the future during the Prometheus mission. They seem to understand the powerful and "usefull" nature of the Xenomorph DNA maybe even admire it and it's genetic strength. With that in mind we assume they go on to explore the possibilities of the DNA within the Alien Xenomorph. Why they left the rest eggs etc who knows? but again this is ancient history. They took the queen, or an egg or eggs for research and left. This for now explain and ends the original derelict Sj Canon till the Nostromo Crew encounter it. So the Sj have this genetic material and distil it to create "Eu De Alien" otherwise known as black goo... They do this because they worked out the Alien Xenomorph's DNA could combine with it's host to create the best assumed combination of itself and host for the environment it finds itself in. That's how they seed earth, by consuming the "Eu De Alien" rather than being impregnated by an ofspring of it... the dna itself seemed alive in the water and created something new from the Sj Kamikazee Engineer.... it created humans as we know and love them. This would also fit with why the worms turned into alien worm... they were alive already a basic life form then mutated by the goo from swimming in it and they follow worm like parasitic tendancies, they just create more alien worms not alien human worms... as they are already an evolved form of worm they live to be like themselves unlike the pure "Eu De Alien" which lives to fuse or change what it contacts. This would also fit with why Fifield changes, you see he wasn't directly attacked he fell face down in a bath of "Eu De Alien" with a broken helmet... So if you encounter the "Eu De Alien" GOO you change, maybe into a more violent version of your species. The worms change to Cobra Alien freaks and Fifield goes nuts and tries to kill every one. This all fits quite well with the percieved properties of the black goo. Charlie only has a tiny bit of black goo with his champers so takes longer to change, and before full change impregnates Shaw, making a proto-face hugger "Eu De Alien - Human" hybrid which results in the tentacled body hugger step in the erratic lifecycle of alien, this then goes on to hug a Sj and creates something similar to it's "Original Xenomorph Form" depected in the Mural. But this xenomorph version is not the version we see in Alien this one is a form based more on human embryo based body hugger impregnating a space jockey. To recap. The Xenomorph in Alien lifecycle is... GENESIS UNKNOWN - Bust from SJ, lay eggs, Face hug human, chest bust = ALIEN The Xenomorph in Prometheus is... Goo slowly infects human, makes other human pregnant, body hugs a Sj, Chest busts fully grown from Sj. Fifield Gos feral and nuts cos he encountered a lot of the goo. The worms become cobra aliens because the encounted a lot of the goo. Charlie changes slowly cos he encountered a bit of the goo. The seeder Sj on earth erupts into raw dna in the water because his goo was "just right" and no doubt an intended consequence. So the derelict is still ancient history, the Sj have been messing about with "Eu De Alien" for years since and seeded earth ect.. then simply have an accident by creating something unexpected or unplanned such is the established survival nature of the xenomorph or xenomorph dna. So the Prometheus story line and all associated creatures from the cobra to the body hugger all make a kind of sense in that the Xenomorph DNA and accociated creatures are all hardy, violent and adaptable... "it's adaptability matched only by it's hostility" I think Ash said in Alien. Something the Sj liked about it perhaps.. and why they made the goo in the first place. The Alien storyline it it's own story line and has it's origins in the ancient history of the Sj rather than the later history where they have learned to utilise Alien DNA to make the Goo... The real "Prometheus" is the SJ Race, they got the Xeno DNA they did good with it like created humans ect but eventually it bit them on the ass... or raped their faces... you choose.