I'm not exactly sure but if you prepare an SD card with Hekate and add the ChoiDuJoirNX.nro to the 'switch' folder, you seem to be able to start it from the Tools menu.
For upgrading you also need the firmware on that SD card.
There is also the option of doing it with a PC when all hope is lost :
But I would try Hekate first....
For entering RCM mode you need a jig and payload injector (pc/smartphone/standalone).
Pressing vol- and power should get you into RCM mode.
But I presume you've done that before as you are already on a CFW.