Let me explain in more detail.
You have two important tabs, the user tab, where all your game saves are stored, and the SD tab where your extracted saves are stored (in SD:\savedatafiler). Each tab shows instructions in the top screen.
In general you will be exporting saves from your 3DS to the SD card (This is done with the X button in the user tab). And injecting extracted saves back to the 3DS (Done with A or R+A in the SD tab).
In the case of Pokémon and other games (Animal Crossing, Tomodachi Life), there's something called "secure value" that prevents saves from working when the secure value doesn't match the save, if you import an old Pokémon save the secure value will not match and will result in a "Save data is corrupted" when you start the game, to solve this, you have to go to the user tab and locate your Pokémon titleid in the list, in there, the combination of buttons R+X will delete the actual secure value, since the game won't have a secure value it will automatically create one with the actual save.
Long story short, whenever you import your Pokemon saves you have to make sure to delete the secure value. This post was very old actually, right now there's another application called JKSaveManager which does this automatically.
Thank you, it worked for me with JKSaveManager. All I had to do was to export save from CTR -> An then select CIA version from Pokemon and import. FINISH!! Thank you so much! Now my GW Cart is useless