Tokeegee

For four hours now, I've been trying to randomize a pokemon y rom (I started with a .cia file because it seemed like people used those) I got all the way up to the point where I randomized all the wild pokemon in PK3ds, but I have no idea how to remake my rom again. Every tutorial I see has people setting it up to play on their 3ds and I just want to emulate it. Anyone have any ideas, I have a real headache at this point...