Actually, there's not a whole lot in the way of "readiness" needed for SH3 Commander.
It's a program that runs outside of SH3 - you launch it prior to playing (it even has a Launch SH3 button). It generates alot of really neat stuff, giving your Kaleun a background, allowing you to give out more than the alotted medals, promote all who are of experience instead of only 2 or 3, etc.
It's really very handy and pretty cool!