SH3 Commander is a stand-alone program, not a mod. It doesn't matter when you install it. You launch Commander, select the options you want, set up a new career (if necessary) in Commander, then launch SH3 from within Commander, by clicking the "Launch SH3!" button. Commander does its file-modding, then initializes SH3. When you exit SH3 (as you normally would), Commander restarts, and either removes the file-changes automatically or when you click the "Rollback SH3" button.
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