Cloning in Emerald is pretty easy, just don't try it on Fire Red OR Leaf Green. It will mess up your game Well, to clone, you need to have access to the Battle Tower. If you do, then great! ^^ I'll tell you the instructions.
1. Go to the PC and deposit the pokemon you want to clone into an empty box.
2. Save your game.
3. Withdraw your pokemon
4. Talk to the lady that offers you to battle other trainers with your friend.
5. She will ask you to save your game.
6. Now, when she asks you "would you like to save your game?" DO NOT DO ANYTHING BUT RESTART THE GAME (which is pressing the A,B, Start, and Select buttons at the same time)
7. Now, turn back on your game and do your usual thing, I don't think I have to explain it ^^
8. You should be saved infront of the lady and your pokemon should be in your party
9. Now go to your PC and find the box that you saved your pokemon in...and walla! its there!! ^^
10. Any Questions?