just google savedatafiler and bigbluemenu,
1) put the savedatafiler.cia to your big SD card
2) boot bigbluemenu and install savedatafiler.cia ,then it will prompt outside your 3ds background.
3) mount your pokemon game(dont load the game) , then open savedatafiler and export CTR CARD.
4) download pkhex and open it.
5) take out your big sd card and use cardreader to read it on pc,load/open pkhex and find your save file in " filer " folder, click the " main " (this is your save file),then u can edit/clone your stuffs ,but if u edit out nonlegit pokemon ,u cant trade/battle it online.
6) after done clone/edit , save it and then put your big sd card back to your 3ds ,open savedatafiler again and import your save file.
7) play your pokemon game , profit.
this is just a simplify guide,because i am not every good in explaination ,what i did was i manually doing it without read the long tutorial.