here is what you do. make sure you have a master ball.
First go to the battle tower in the battle frontier. Give the master ball to a pokemon then go inside. Go to the PC and deposit the pokemon with the master ball. Save it and withdraw it. Talk to the lady that does the Link Multi Battle Rooms(she is the closest to you). Do a challenge(Lv. 50 Or open level)and choose the two pokemon.She will ask you if you want to save it. Say yes, and when it says 'there is a saved file. is it ok to overwrite it' turn the game off. Look in your party and then look in the PC.the pokemon will be cloned and so will the master ball. If you want more you have to have a lot of patience.