How to explain this in Alien and Prometheus considering Alien Covenant plot?

You are assuming that all the engineers were wiped out with David's attack.

This is obviously not the case though since we know that the Engineers have been colonizing worlds and setting up bases from the movie Prometheus.

Further we don't even know if all the Engineers are dead on the planet in Covenant. We just know one of the cities and probably several miles around the city is barren of life.

This is the very question I had after seeing Alien: Covenant. How to get from end of Covenant to Start of Alien? If the narrative is that David created the Face hugger & Xenomorph that we all know and love then this creates a huge continuity error given the mural on the wall in Prometheus is ‘our’ Xenomorph. I think the comment by Alex is interesting in that other Engineers capture David and his creations, however it does not explain the length of time the crashed ship was on LV-426 before the discovery of it and its (David created) egg cargo (Quote by Dallas “it looks like it’s been dead a long time, fossilised; looks like it’s grown out of the chair”). Having looked at the timelines, Prometheus (2093), Covenant (+10yrs, 2103), Alien (2122) so assuming another Engineer captures David’s creations quickly after Covenant and there was time to make hundreds of eggs, there is still only 19yrs between Covenant and Alien. Not enough time to achieve the fossilised condition of the dead Engineer on LV-426. Of course we could just assume that the Engineers have also created the same creature version just a lot sooner than David and he has just achieved the same but a lot later... that might solve it!

I don't know for certain if the comics, Fire and Stone are canon, but one of the stories take place at the same time as Aliens and features a crew member finding a dormant Engineer in stasis on LV-223

Set concurrently around the same time as Aliens, the narrative begins prior to the arrival of the colonial marines as seen in the film, during the Xenomorph infestation of the Hadley's Hope colony on LV-426...

As Cale and Dione continue to bicker over the group's course of action, and the xenomorphs continue to whittle down the group's numbers, Russell becomes increasingly distant from the group affairs. Having stumbled upon a probe from the Prometheus expedition decades ago, Russell analyzes the data from the probe and finds that the current landscape of LV-223 has changed drastically from what it was at the time of the previous expedition. Russell deduces that the enigmatic black substance that the members of the Prometheus expedition encountered acted as a catalyst that expedited the evolution of the environment on the planet from a barren, rocky wasteland to a lush jungle setting. Russell also explores a crashed ship of the "Engineer" species encountered in the film, and finds a dormant Engineer in stasis, although much to his dismay, he is unable to wake it. Russell continues to compile his findings and stores notes and work in a cave situated within a mountain that the xenomorphs are wary of approaching. Although he reports his discoveries to the group, Russell's findings are dismissed as unimportant in comparison to the immediate goal of survival.

https://en.wikipedia.org/wiki/Fire_and_Stone

So although this may or may not be considered cannon, we *might presume that there is at least one Engineer alive, despite it is inactive post Alien Covenant.

The comics are also suppose to be crossover event between various Alien/Predator/Prometheus series. They connections between planets here with this crew, it may hint at further revelations down the road.

Given 'Alien: Covenant' fits into the established continuity as it is a direct sequel to 'Prometheus' which was intended to be the first of a prequel series of films that led to 1979's 'Alien' I would assume based on the presented evidence that David is not the original creator of the Xenomorph species. As other responses have said you are assuming that all the Engineer's in existence were wiped out when David jettisoned the juggernaut's payload. All we see is a single Engineer city and a specific section of Planet 4 in the movie and so we cannot say with absolute certainty that David wiped out the Engineers. Given the nature of the pathogen within the black goo and the creatures spawned from it and David's experiments I would think it safe to assume that all non-botanical life on Planet 4 is extinct. It is true we can't be sure but we do know David has been on Planet 4 for 10 years and it would be peculiar for other Engineer populations to not have been aware of him or bothered to check out a city that suddenly went silent within that time.

We also know the Engineers colonise other worlds from 'Prometheus' where their structures show obvious signs of terraforming, it could also be assumed that Planet 4 itself was not the Engineer's actual homeworld but a colony planet that had established itself well enough as a base for the Engineer's to conduct further expeditions which could be inferred from the lack of any other structures on the planet besides the city itself and Oram's expedition from the dropship to Shaw's juggernaut taking approximately a day (at the least several hours) there and back to perform and in all that time they didn't discover any sort of structure, not even the Engineer city. Also we have seen the juggernaut ships themselves carry different cargos. The Space Jockey's ship contained thousands of Xenomorph eggs whilst the one's present on the nearby moon LV-223 carried vases containing the black goo pathogen and were determined by the crew of the Prometheus to be part of a military operation bound for Earth. I think it is probably safe to assume that there are more Engineer planets out there and it is possible we haven't seen their homeworld either.

You've sort of provided answers within your own question as well. You mentioned the mural that appears in 'Prometheus' that depicts what looks to be an obvious depiction of the Xenomorph. This could be construed as some sort of precursor species such as the Protomorph that has been thrown around by the production crew of both 'Alien: Covenant' (regarding the Planet 4 Xenomorphs) and 'Prometheus' (regarding the deacon). It could also be an Ultramorph (a concept from Jon Spaihts' original script refering to a Xenomorph birthed from an Engineer) though the design is much closer to the classic Xenomorph. With this present in the film directly proceeding 'Alien: Covenant' I can't see any reason to think David is the originator of the Xenomorph species. We already know in the film itself that the monstrosities David crafted were in fact results of his experiments with the black goo which itself was created by the Engineers for both military purposes and seeding life on planets.

David considers himself a God for creating life and manipulating the black goo to create 'the perfect organism' but everything he uses to do so has been provided for him. The black goo and its nightmarish effects are a result of the Engineers. His monstrous creations brought about due to genetic experimentation with Engineers and Elizabeth Shaw. There's no evidence presented in 'Alien: Covenant' that indicates that Engineers have not already conducted their own experiments with the black goo and created Xenomorphs. The Last Engineer in 'Prometheus' seems to know exactly what the trilobite is and what it will do to him if he fails to fight it off. He would also be aware of the mural and shows no real surprise when he discovers the trilobite, his shock pertaining more towards one being present in Vickers' lifeboat than it being an unknown lifeform. This would suggest he is aware of the creature and its life cycle. Given most of the creatures created by the black goo share traits of Xenomorphs, the trilobite is in essence a gigantic facehugger, the deacon a form of Xenomorph. The bloodburster is similar to a chestburster. The Neomorph is a more animalistic version of the Xenomorph. From what we see in both movies it indicates that the Engineers know exactly what the black goo is capable of and so it could be further seen that they would know what it can create.

Finally the other big contradiction to David being the originator of the species is the Space Jockey in 'Alien.' When the crew of the Nostromo arrive on LV-426 and enter the Derelict ship they come across the corpse of this Engineer with his chest burst open. It is noted by the crew members present in the same scene that the body is fossilised. A fossil is defined as the remains or traces of an organism that died more than 10,000 years prior. This would mean the Space Jockey is at least 10,000 years old by the time of 'Alien' and it would therefore be safe to assume it is in this condition at the time of 'Alien: Covenant' which is set 18 years before the events of 'Alien' then David cannot be the originator of the Xenomorph species. This of course would add further irony to David's character and his capacity to make mistakes that is played with in Covenant by establishing his God complex is founded on him creating a lifeform that already exists. Since the eggs present on the derelict ship are at least 10,000 years old, due to them being kept in a form of stasis (similar to that which Ripley herself is preserved by for 57 years without aging), then David cannot possibly have been the creator of the Xenomorph species since there are specimens within the franchise universe that date back far longer than David himself has been alive and so he cannot be their creator.

Whether Ridley Scott completely intended David to be their creator or not when he made Covenant I don't know but if a third movie were to be made that somehow results in David discovering that Xenomorphs already exist despite his belief that he created them it would be a nice irony that continues to build off that established in Covenant where he reveals himself capable of making mistakes such as attributing 'Ozymandias' to Byron only to be corrected by Walter informing him it is actually by Shelley and that he also fails to examine the deeper meaning of something or acknowledge it when it doesn't fit his ideology. Again to use 'Ozymandias' David fixates on one specific aspect of the poem that feeds his God complex ('Look on my works, ye mighty, and despair') only for Walter to recite the final verses of the poem that reveal that the mighty works of Ozymandias have long since been buried by the desert sands and there is nothing but isolation left. For David to discover he isn't what he believes himself to be in a third film would be an interesting way to complete his story arc.