You said you wanted to be able to click on a smaller window, and have it swap to a larger region (in your image, 2 - 13 would swap with 1 and 15-26 would swap with 14). As MiRai said, this is pretty much the default behaviour, and if it is not working for you, then you need to explain what about it is not working, and probably share your profile http://www.isboxer.com/wiki/Configuration_Sharing
And now you don't want to swap when clicking only on a certain portion?. Going to say you wont get all your wishes in this world, because that sounds damn tricky. Have it swap when certain portions of a window are clicked on but not others. It probably could be done with VideoFX, but that would require synchronising the resolutions, which you've indicated you don't want to do because of performance reasons (although the obvious choice would be to get better hardware and not run on a hamster in a shoebox)
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