(You must beat Elite Four first)
1. Save in front of the PC at the Battle Tower
2. Deposit the Pokemon you want to clone
3. Save again
4. Withdraw that same Pokemon
5. Go to the Link Multi Battle Lady
6. Select your two Pokemon, then when she asks if you want to save your game, say yes.
7. When the "Do you want to overwrite?" message appears, press A,B,Select, and Start or just restart you GBA or VBA.
There simple as ABC