>>50090204>How do Pokeballs work?If i remember the PLA reveals right they don't actually shrink a Pokémon, but rather exploits the fact Pokémon have shrinking as a innate ability (That is arguably how they can hide in tall grass and why they "shrink away" when fainted in the games), the actual thing the balls do is soothe it presumably using a Tumblestone or variant of it, like the Origin Ore. and Legendaries at least have the ability to "break free" even if caught should they feel like it (IE: Their trainer dies) and they are just tagging along for the hell of it, even with their powers limited by the Pokéball (Arguably because they don't wanna break the ball by accident).
My impression from how PLA handled it is basically that Pokéballs are super comfy for Pokémon and that is how they "catch" because you basically both prove your strength in battle, and then offer up a nice "nest", and over the series Pokémon do seem to be able to know what is going on outside the ball and leave it should they so desire even without prompt from their trainer, though i think that is kinda inconsistent.
As for the keeping track of the balls thing, it's basically up to the trainer, we know some trainer customize their balls to keep track, and not that many people actually even reach having 6 Pokémon, i assume the Player Characters are just that good at memorizing which ball has what since you always play as a prodigy. I think that is how it goes at least.