First you have to go to the online updater and update all of your configuration files, core files, assets, everything and restart, but then you can simply go to the online updater and download any emulator core for any system.
I am playing on MelonDS which requires one fix to use the touchscreen in-game:
Core options -> screen -> change first option to Touch.
Also for pokemon specifically to have save filed work properly, you have to download a nintendoDS BIOS blob and put it in one of your retroarch folders. There are guides on that.
A little bit of configuration, bit you essentially have every single open source emulator in one app.