Go to the pal park in Fuchsia City. It's where the Safari zone was in the original. There, you can participate in a "catching contest" in which you are given 6 sport balls and try to catch 6 pokemon- the ones you just migrated. Fortunately, the sport balls don't fail, and you don't have to battle the pokemon, so it's an easy catch. Just make sure you bring surf for water pokemon.