If you download a mod and it has extension a2, a3 or a4, move the file to ModifiedFiles directory in Mod Installer:

The ModifiedFiles folder name depends on for what FC game the mod is created, so for example:

Some mods like Winter Hope County or Libertad mod has own modpack bin file.

To add it to Mod Installer, simply put the file into the same as Mod Installer exe file. Just like this: