Commander is not a mod, it's a standalone program. Save the download somewhere else on your hard drive, not in your game installation.
Extract to some other location on your hard drive as well, run the .exe file - probably setup.exe - to install Commander. You can install it anywhere on your hard drive, but it does not need to go in your game installation and I would not recommend putting it there.
When you open Commander you will need to point it to your existing game installation so it knows what files and folders to work with.
There is a user guide that will be included with your Commander installation, it is brief and will answer most if not all of your basic questions on what it does and how to set it up to work with your game.
