Of course, the easier way is just to install SH3Cmdr once and copy and paste it as many times as you want, in much the same way as you'd make multiple copies of SH3 itself.
Then, all you need do is run each SH3Cmdr installation and manually point it to the SH3 installation that you want to use it with (as explained in the User Guide). Create shortcuts on your desktop with meaningful names (ie "SH3Cmdr - GWX", "SH3Cmdr - NYGM" etc) and you're set; you'll have a copy of SH3Cmdr dedicated to each installation of SH3.
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