First you need to go to Nexusmods and register. Registration is required in order to be able to download modifications.
After registration we going to Sheltered 2 section. Here we can choose mod and download it.
As example we try to install very useful mod Automatons that reduces micromanagement. We choose that mod and going to files tab and click manual download.
Nexus will say that some files are needed for the mod, namely bepinex and confmanager. Click on links and download that files then download Automatons.
After download we going to our steam library/steamapps/common/Sheltered 2 and unzip bepinex archive to the root of the folder. Your root folder should look something like this:
After this go to BepInEx/plugins and unpack downloaded Automatons and ConfigurationManager files.
At this point the installation is complete and you can launch game. In game press configuration key (default F1), press on Automatons and configure it.