Here you will find a step by step guide on how to beat Pokémon Colosseum.
The round-bracketted pokemons of the trainers refer to the ones they use to fill in the space of the dark pokemons when you rebattle them. The square-bracketted ones refer to the ones that they possess later on (due to new capture or evolution).
This Walkthrough is very text intensive and will soon be updated with Pictures to make it easier to read