Install sys botbase - Manu098vm/Sys-EncounterBot.NET GitHub Wiki
Download the official sys-botbase and copy the atmosphere folder to the root of your SD card. Since Sys-EncounterBot 2.5, LGPE users do not need to download a different sys-botbase version anymore.
(Only if you want to use bots for Sword and Shield) - Download the Anubis's Fork of ldn-mitm and copy the contents to the root of your SD card.
Reboot your Switch to CFW and go to the internet settings. Take a note of the IP Address of your Nintendo Switch, this should be added to the configuration when setting up a bot together with port 6000.