Yes, SH3 Commander is an external mod. You launch it before you launch SH3 (Commander even has a Launch SH3 button to simplify the process) and change things via the menus.
Very intuitive and fun to use - as it's external, there's next to nothing you can do that will screw up your game (that is unless you try to promote, award, etc. your crew while still at sea...).
You can even assign your own patrol zones.
