Download the mod and put in in your MODS folder in your Nuclear Throne Together folder. Open NuclearThroneTogether.exe and, in the character screen, write in the chat (T):
if the mod is one file:
/loadmod (name of the mod).
If is a folder, it has a main.txt. So put:
/load (folder)/main.txt.
If you want to make it load automatically everytime, create in your MODS folder a "startup.txt" file and put the commands in it.