Go to where your mods are located, right click on the game and go to mod folder path.
D:\Citron-windows-stable-01c042048-x64\user\load\010019A01E2F2000\
Metroid Prime 4 Title ID is 010019A01E2F2000 and Build ID 8275FBE1EC5191C2 are what im using in my example.
In this directory create a folder called mods. Then inside of this folder is where your cheats go. Its tedious on Cintron, I had to set up each individual cheat to work. so here is an example.
Z:\Citron-windows-stable-01c042048-x64\user\load\010019A01E2F2000\mods\Infinite Health\cheats\8275FBE1EC5191C2.txt file with the single cheat
So I had to create a folder for each cheat, so for infinite Missiles it still be under mods folder but in its own sub folder, so Mods\(cheat name folder)\cheats\(build ID .text file)