This issue (no control for lower screen possible) persists already since Version 5.22, see my post here:
It is because since 5.22 only the standalone core of citra is available.
Before in older versions (5.21 and older) it was possible to select to the Libretro Citra Emulator (in Game Settings, Advanced, 3DS) and there you could configure the controls and other settings within RetroArch Quick Menu (Hotkey + B while in game).
nadenislamarre will there be the possibility to configure the citra emulator in the future? because in Applications (F1 on Keyboard) there is no citra-emu-config yet.
Or maybe the Libretro Citra Emulator could be implemented again? Because 3DS looks better with bezels (only available with libretro emulators) and you can easily edit configuration via RetroArch Quick Menu (activate control for lower screen, enhance resolution etc.)