There's a readme that comes with JSGME that tells you what to do. You basically install it seperate, but it'll tell you to do a thing or two with folders in the SHIII folders. All that does is allow what mods you've installed with it to be located easily and for the program to install/uninstall them.
I have it myself and it works wonders. I play online with some people that I'm in a realism unit for Call of Duty 2 and they don't have any mods installed. The Program makes it easy for me to rollback the game to stock SHIII so I can play with them and then when I'm done I put them back in.
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