Commander isn't a mod, so it shouldn't be in your game MODS folder.
Did you extract a downloaded zip file for it into your MODS folder, maybe?
What you get when you extract the downloaded zip file for Commander, IIRC, is the documentation for installation plus the files needed to install it. The setup.exe file will install Commander, but again - it's a standalone program, not a game mod per se, so it shouldn't really be in your MODS folder. It's not something you'll be instaling
into the game, you'll be using it outside the game to make selected changes in some gameplay settings and to manage your career.
The other set of files you describe sounds like the config files for Commander 3.2 + GWX, if so that's not for your game MODS folder either. If it's what I think it is, it's a self-installer that adds a couple small things to Commander to make it work much mo' better with GWX3.
So - whatever you've downloaded for Commander (including those config files) and extracted into your MODS folder, I'd delete that stuff from your MODS folder and extract that stuff somewhere else on your hard drive and proceed from there.
Run the setup.exe for Commander first to install it. Then run the little self-installer .exe file for the Commander/GWX3 config files and let it do what it needs to do to set up Commander to run properly with GWX3.
