You mean the control of the lower screen?
In Batocera 5.22 only Standalone Citra is available.
If you want Libretro Citra (where you can press Hotkey + B while in game, to open up RetroArch Quick Menu to change various settings and to be able to control the lower screen with right Analog-Stick) you have to use Batocera 5.21 and change Emulator to Libretro and Core to Citra in "Game Settings", "Advanced", "Nintendo 3DS".
I hope in one of the next versions (5.23 or 5.24) there will be a Citra version, where you can configure the controls of the lower screen (again). One of the devs is testing another Citra Version (Citra qt) at the moment and maybe it will be integrated in 5.23 already, so just be patient and use 5.21 so far 😉