OK. What you need to do is create two *new* shortcuts to SH3Cmdr.exe, with the /l: switch added. For example,
"C:\<Path>\SH3 Commander\SH3Cmdr.exe" /l:"C:\<InstallPath>\SilentHunterIII - NYGM"
"C:\<Path>\SH3 Commander\SH3Cmdr.exe" /l:"C:\<InstallPath>\SilentHunterIII - GW"
This forces SH3Cmdr to use these locations rather than use the one stored in the Registry (ie the original installation path).
To create the shortcuts, just right click somewhere on your desktop, select New|Shortcut and enter the location as above, press Next then enter a suitable name, then press Finish. Done.
Then, all you need do is click the icon for the version of SH3 that you want to play. SH3Cmdr does the rest.
ONE warning though. If you run "SH3 - NYGM" then want to run "SH3 - GW" afterwards, you MUST first rollback SH3 - NYGM, otherwise, when you run SH3 - GW, you will cross pollenate it with NYGM files. For example:
ALWAYS
-Run SH3Cmdr NYGM shortcut
-Play game
-ROLLBACK SH3Cmdr NYGM
-Run SH3Cmdr GW shortcut
-Play game
-ROLLBACK SH3Cmdr GW
NEVER
-Run SH3Cmdr NYGM shortcut
-Play game
-Run SH3Cmdr GW shortcut
-Play game
Alternatively, you can install (or copy) SH3Cmdr again to a different location. Then, you can point one shortcut to SH3Cmdr installation #1, and the other to SH3Cmdr installation #2. Then you will not have this rollback problem. For example:
"C:\<Path>\SH3 Commander Copy 1\SH3Cmdr.exe" /l:"C:\<InstallPath>\SilentHunterIII - NYGM"
"C:\<Path>\SH3 Commander Copy 2\SH3Cmdr.exe" /l:"C:\<InstallPath>\SilentHunterIII - GW"
The problem with this approach though is that your SH3Cmdr.ini files will get out of sync with each other. But that's prolly less of a problem than your whole game getting out of sync!
But I'd only recommend this second approach if you think the first approach will cause problems for you.