This took me about a day to do.....
what you have tfdo is grow a sceptile untill it learns false swipe....put sceptile first pokemon.....then when you find latios for first time or by hunting him down with pokedex, use false swipe......if you dont get his health all the way down....dont worry becouse if you find him again (using pokedex)he will have the same HP you took away...=] leave him with 1 HP then get a pokemon with "mean look" and a move that brings the pokemon to sleep .....keep using that and ultra balls and you'l have latios in a few tries. i hope you liked this hint. and if you wana make it all faster......use ultra balls on groudon
and save the masterball for latios.