As U Crank said, Commander is not a mod at all. It's a tool that lets you control a great many functions from outside the game, and is completely independent of normal mods. It works well with any supermod, or no mods at all.
Would you like to change the deck gun reload speed? The wave height? Other parameters? Would you like for your crew names to be chosen from almost two billion name combinations? Would you like to choose your own patrol grids before the game is loaded? Would you like for the ships you sink to have actual names, cargo listings and crew numbers, including number lost in the attack? Dozens of other features I can't remember off the top of my head?
Give it a try. You'll thank us (and JScones) later.
