https://gbatemp.net/threads/tutorial-installing-rxtools-custom-firmware-3ds-and-2ds.390867/how do i set up rxtools and update emunand?
Get this set up, and when you're positive you're in emunand go to your system settings and update your firmware.
You'll know you're in emunand if it shows like RXsomethingsomething-yourfirmware instead of the 9.2.whatever-whatever(REGION).