I think they memorise the order before going on their journey.

Some Trainers actually physically mark their Poké Balls. (I recall a Trainer from the anime doing this, I just can't remember who…)

That was just my theory. And there are a few scenes in the manga where the balls are depicted as transparent but thats the manga sooo....

It's like how Pikachu's pokeball had a little lightning bolt on it, they just mark it with something that has to do with the pokemon inside

Yeah, but Ash didn't put that on himself.

We never see him do it to the other pokeballs but I think he just does it off camera