This guide can be followed on either Linux or Windows distros, with the exception of the launch option at the end which is exclusively needed on Linux based operating systems.
All you need to do to mod Lethal Company is to move the folder "BepInEx" and the files "doorstop_config.ini" and "winhttp.dll" from BepInEx_win_x64_version-number.zip into your "common/Lethal Company" which you can easily navigate to by right-clicking the game in your Steam library, clicking "Properties", then clicking "Installed Files", and lastly clicking "Browse..."
If you're on Linux, you still need to get the "win" BepInEx version as the game is ran through Wine. You will also need the launch options:
WINEDLLOVERRIDES="winhttp.dll=n,b" %command%
Then if you want to install mods, all you have to do is download your mod like notnotnotswipez's MoreCompany mod and merge the BepInEx folder located in the download with the one already in your "common/Lethal Company" folder.
If you want to remove any mods, check the files that come out of the original .zip download and remove them from your BepInEx folder, e.g. For MoreCompany, you would remove the file "common/Lethal Company/BepInEx/plugins/MoreCompany.dll".
Happy Lethalling! Also credit to: Jonathan Gene's Guide on YouTube!