Yup, I solved it. Turns out I did not update my godmode9 so the option for agsb.bin is missing previously, I was mislead in assuming the format needed is different. Update godmode9 guys, then follow the guide in 3ds.hacks, it's that easy actually.
Also I wanna share my experience in using this, 3 games I've played for at least couple of hours each got their saves corrupted at the end sadly. 2 of them crashed randomly while one of them having serious slowdowns (MMBN3). Cheats had also been tested before in pc (they're okay except MMBN) and accordingly to the rules (no master code, no blank choice codes). Personally I think the best choice is to mod your saves beforehand or just apply cheats in it using your emulator then inject that saves like above. Game on a clean slate with no fear of losing your progress.