Game modding with LayeredFS
LayeredFS, a tool built in to Atmosphere, allows you to replace game files with your own.
Make a folder on your SD card inside the
atmosphere/contents/ folder, with the name being the title ID of the game you would like to replace the files of. Note: On Atmosphere 0.9.4 and below
contents is called
Switch game title IDs can be found on http://nswdb.com/. If you have a pre-made mod, the files would be placed here. Then, once the title is launched while in Atmosphere, your mod should load.
Batman in BOTW