I recently watched Alien, Aliens, Prometheus, Predator, Predator 2, Predators and both AvP movies.
From what I see (and it will be hard to sway me), all of the series are linked. With the timeline going ROUGHLY in this order...
Predator
Predator 2
Predators
AvP
AvP: Requiem
Prometheus
Alien
Aliens
Alien 3
Alien Resurrection
(note that I have not seen Alien 3 or Resurrection in years, just going off memory.
I don't know much about the story behind the Yautja and the Engineers, but I think it goes along the line of;
Possibility ONE.
The Engineers are serving the Yautja, forced to make sustainable hunting grounds.
The Yautja would have used the Engineers for breeding Xenomorphs before the humans were created by the Engineers.
Possibility TWO.
The Predators have some sort of quarrel with the Engineers, being the two most dominant species around.
I, for one... Hope that all of the series are linked and hope that in the future, they bind it all together in a movie, multiple movies or T.V. series.
(To answer the question of who would win between the Engineers and the Yautja... I would say the Yautja. Especially if fighting together, species against species).