How do trainers know which pokemon are in which pokeball? I know about the new sticker function in D/P, but meh.

Erm, I don't really understand your question here. o_o

If you're asking how your trainer would, generally they have some way of defining them. In one episode of the Anime, there was a guy who put labels on them so he could tell which held what Pokemon. In the Manga they're transparent so you can see the Pokemon inside. Perhaps it's intuition or remembering which is in what order on your utility belt.

Or maybe in the game, you put them in order.
In the anime...I dunno, its just random....

I dunno, I always thought trainers could somehow sense which Pokemon is in what Pokeball.

...or maybe it is a kids' show. Seriously, you have to draw the line somewere...

In te games, I at least kow where my pk mn are, as I have a little sysem, lke, my Flying types are ALWAYS at the bottom, so I have a two down A down A access to Fly...