So where did David find all those engineers to kill in Alien: Covenant? Is it the same planet where Elizabeth and David were stranded and then was found in Alien: Covenant? And if it is why did they find only one engineer in Prometheus?
Elizabeth and David were never stranded. The final shot of Prometheus is of them exiting the planet to go to "where THEY came from." The planet in Alien: Covenant is where they ended up. Presumably, David incapacitated Elizabeth on the journey there and decided to kill all of the "engineers" with the pathogen they created when he finally reached their home world.
There's a lot of things Prometheus doesn't explore. At the end of the film, David indicates that there are other ships for the protagonists to use to get off of the planet. There might be other Engineers in stasis somewhere. That's probably doubtful, but it's a possibility.
Also, Elizabeth Shaw indicates that she does not want to go back to earth (David's suggestion), instead she wants to go to their world. So, presumably, David and Elizabeth end up on the Engineer's home world as Dylan indicates.
Shaw recovers David's remains, and with his help, launches another Engineer spacecraft. She intends to reach the Engineers' homeworld in an attempt to understand why they wanted to destroy humanity.
https://www.alienuniverse.com/post/prologue-the-crossing contains a short from the official site where we hear from David that they left the planet, and it shows them arriving at the Engineer homeworld.
According to me Shaw and David actually reached the planet where the engineered humans existed. But David due to obsession with his discovery of new human alien species kills Shaw by giving her a pathogenic drink and after reaching the planet deliberately unleashes the pathogenic liquid on the residents of that planet due to which mass killing occurs and therefore the planet becomes desolate. The planet is same on which alien covenant crew members landed.