The best way to figure out how they work is to try to write one yourself, or look to see how other people do it. Clearly, if it's a story you don't want it to look like
Charmander used Scratch on Rattata! Super effective! Rattata used Tail Whip! Charmander's defence went down! Charmander used Ember! Rattata fainted! Charmander gained 75 epx points! Charmander evolved into Charmeleon!
As mentioned, it is extremely dull and you might as well play the game instead of reading the story in such a case. Read books, see how other similar scenes are done and think it over. It's really not compliacted.
For a battle scene, you just need to know what Pokémon are fighting, their attitudes/personalities (which will effect the way they fight), what attacks they know/like to use, their Trainers (if they have one) and the location. Then just start writing out what would happen.
Really, there's nothing more to be said. You were much too vague in making this thread so there's no way to really help you. It's a pretty useless topic, so I'm just going to close it. Simply look around and think about what a Pokémon battle would look like and you'll eventually figure something out.
~Psychic