The Commander is a standalone prog and you can install it before or after SH3/GWX. You have the correct files for it. As I understand it your SH3 install is clean and unmodded, so I would delete any careers you have running and then make a copy of the SilentHunterIII folder and save that copy somewhere else.
Then run the GWX.exe file, then when GWX is installed, run the GWX103.exe file to update GWX. After that run SH3Cmdr27.exe to install the Commander. Then unzip the GWX102CfgSH3Cmdr.zip file directly into the SH3 Commander\Cfg folder.
I recommend you to read the help and fac files for the Commander before you use it. Same goes for the GWX manual, itīs well worth the time
