Some requirements for cloning in Pokémon Emerald are that you need to be in the end-game, you must have defeated the elite 4, and have access to the Battlefrontier.
Step 1: Enter the Battletower.
Step 2: Go to the top right to the PC and deposit the Pokémon you want to clone in the box. (preferably an empty box)
Step 3: Close the PC and save your game.
Step 4: Walk to the nearest counter and talk to the NPC. Go through the conversation, she will ask if you want to participate in the Battletower Challenge. Accept this and choose two Pokémon.
Step 5: She will ask if you want to save the game. Select ''YES''.
Step 6: CAUTION, while saving the game, you must turn off the GBA/NDS immediately! So not after saving but during saving.
Step 7: Restart your game, you will see that the cloned Pokémon is in your party and in your box!
For more explanation, follow the video below of Pokémon Emerald Version!