Sure so I use HackingToolKit3ds you run that program then it tells you if you want to extract or rebuild your .3ds or CIA files, you extract your FE Fates Files then when it ends your game is separated in different files, one is gonna be named romds, then you can follow the guide on how to use the randomizer, when you're finished, you run HackingToolKit3ds again and use to Rebuild function this time, then you're done, you can use this new .3ds file and it's gonna be randomized, sorry if it's not clear enough English is not my first language so if you need more explanation you can send me a message and I'll try to make a step by step guide with pictures for you 🙂
Good luck!