okay so I thought I'd share my method of doing this using menuhax, which usually worked after 2-3 times (I installed, pokemon X, Smash Bros., Majora's Mask and it never took more than 5 times trying) using N3ds 10.3.0.28E
once you placed the FBI files and the folder in the 3ds folder on your sd-card follow these steps
1. download your desired .cia file from "that iso site" (make sure it's .cia and the right region)
2. place it on the root of your sd
3. boot into the homebrew launcher through menuhax
4. navigate to the 3d testing software and open it
5. once opened let it stay opened for a few seconds (around 4 secs)
6. close it by pressing start
7. once back in the hb-launcher open ftbrony, once it's open close it by pressing b
8. open FBI and press any button
9. if nothing happens reboot your system by holding down the power button and repeat previous steps
10. choose your .cia file and installation should start right away
11. once finished installing press start as instructed, press start again to return to the hb-launcher
12. your bottom screen will turn red, now turn off your 3ds by holding down the power button and power it back on and let it boot normally
13. your game should sit on your home screen ready to be played