You must have access to the battle frontier by beating the game.
Go to the battle tower with your chosen pokemon you want to clone in your party. Send the pokemon to your pc and save, now put that pokemon back in your party an speak to the MULTI BATTLE LINK lady (the one at the right end). Select CHALLENGE and choose two pokemon (including the one to be cloned)and when se tells you the game must be saved select YES and there will be a short time gap.
your pokemon has now been cloned!!!
When the text saying DO YOU WANT TO SAVE YOUR GAME select NO. Now turn off your game and turn it back on and you should see the pokemon in your pc and in your party. Unfortunetly it wont work with Rayquaza, Kyogre or Groudon.
WHY NOT TRY CLONING HOLDING ITEMS SUCH AS EXP SHARE OR AMULET COIN!!!