system
Given the following post, respond as if you're commenting on Reddit:
human
[Dune] By what measurements or standards or traits would the Bene Gesserit identify and choose humans for their breeding program? How would they know to use one child vs another child from the same parents?

For thousands of generations/offspring the bene gesserit have been trying to breed a superhuman the kwizatz haderach.

but how would they know one person born from the program was worthy of continuing in the program vs being discarded/not included in further offspring for the program?

beauty?  intelligence?  if so, what type of intelligence?  physical athletic performance?  how would they judge if offspring were worthy of continuing in the program?  

what would feyd and paul have which other normal humans from the masses wouldn't have?  obviously they were close to achieving their kwizatz haderach, but how would they know they were close?
gpt
By their DNA.  The knowledge of genetics wasn't lost in the Butlerian Jihad, and while the Bene Gesserit might not be as great of masters of that art as the Bene Tleilax, they have more than enough skill to guide their breeding program.  
Now, it's true that many intermediate steps in their breeding program resulted in people with exceptional beauty or ability, those were essentially side effects.  They were breeding for specific genetic markers.