If you have mods in JSGME that are in the "Activated Mods" window you don't need to start it every time. It will "inject"the mods once you transfer them in to that "Activated Mods" window and they will stay "injected" until you remove them.
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parab's tweaked air strikes => Data => Cfg => airstrike.cfg
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That looks correct to me.
And you say you don't see the difference...well that particular mod will take some time to spot as it is a subtle game play mod, not a graphic mod or anything you would spot directly.