Here are the steps:
1. Power on the 3DS console and insert the 3ds game cartidge that you want to use the save file.
2. Open the gateway menu with “L” , and press “Backup 3ds Game Cartridge”. Make sure the sd card( the one that inside your 3ds console) is big enough to store the save files.
3. After step 2, select “Backup 3ds savegame” to backup savegame. When the process is done, press [A] To Exit. Power off the 3ds and plug the sd card.
4. Open the sd card to your computer. You can see a .3ds file where your .sav files are. This is the rom that was created from your retail game. Rename your “Backup 3ds Game Cartridge” extension from “.3DS” to “.3DZ”.
5. Move the “.3DZ” to the gateway red card micro sd card. ( Do not move the Sav file from the SD card. leave it on the SD card.)
6. Got to
http://3ds.essh.co/ to find the “title ID” of the “Backup 3ds Game Cartridge” . And rename the “Backup 3ds savegame” to the “title ID” of the “Backup 3ds Game Cartridge”, For example, Kingdom hearts NSTC title ID is “000400000008D300″, so its save file should be 000400000008D300.sav .
7. Insert the SD card back into the 3DS. Power on your 3DS and use the gateway 3ds to boot into “Gateway mode”. If you don’t know how to boot into “gateway mode”, you can refer to this article:
How to Instal OMEGA 2.3 for Gateway 3ds card?
8. Select the game you just backed up (the .3DZ file).
9. Your save should automatically restore itself. Then you can play it.