Mid-Patrol Radio Orders is designed to mod Commander itself, not your game installation. Commander is what makes it work.
So, you need to set up JGSME for Commander.
If you already have JSGME set up for the game, open your game folder. Select the following files:
JSGME.exe
JSGME.ini
JoneSoft.txt
Copy those files and paste them into your Commander folder (the one named SH3 Commander that was created when you installed it). Now create a new folder in the Commander folder and name it MODS.
Now right-click on the JSGME.exe you just created in the Commander folder, and drag it to your desktop. Create a shortcut for it there and name it JSGME Commander or whatever you like that will distinguish it from any other JSGME shortcuts you have there.
Now put the mod into the MODS folder you created in the Commander folder, in the same way you would put a mod into your game's MODS folder.
When you double-click that new shortcut, it should open up JSGME for Commander and show you the contents of the MODS folder you just created for it, and you will see the mod you just added and you can enable it in Commander.
For the other mods, I'm guessing that the files they want you to copy into Commander will overwrite the original versions of those files that Commander already contains. So just copy them to the folder where you see Commander already has them and let them overwrite the original versions.
Usually if it says "your SH3 Commander folder" it means the folder referred to above, named SH3 Commander, that was created when you installed Commander.
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