Hoenn treats it like it's a new region. You can go there when you get 4 badges in kanto and begin the Hoenn storyline there. The badges are counted for each region, so you won't be able to just bring a really powerful pokemon and sweep Hoenn with, since it won't listen to you in Hoenn until you have enough badges.
Just something weird from my copy of pokemon black: Shiny timburr is registered in the pokedex, but I have no idea when that was, and I definately don't have it.
carrying net balls would help
I think you can only throw pokeballs at them when there is only one left