this is one way that i know how to clone on emerald:
1. pick the 5 you want to clone with an item if you wish deposit them as the first poke mon in 5 different boxes.
2. Withdraw up to 5 pokemons from a box on the computer
3. Talk to the lady on the far right and choose two pokemons to enter the battle.
4. When she asks you to save you say yes.
5. Then there will be a pause for like about 2 seconds.
6. When it asks you if you would like to save say no and turn off the power.
If you have any other please add it.