How to install mod in Mod Manager - TheLeonX/NSUNS4-ModManager GitHub Wiki

First of all you need to prepare your mod (check this tutorial) and select Game Root folder in Mod Manager:

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After that, you need to drag and drop .nus4/.zip archive into list of mods (or use regular install button).

When you installed mod, it will appear in mod list and then you can press on "Compile mods" button.

After compiling mods, you can run your game and mods should be installed now.