If you build the hack as a small GUI and stick it in the top left, Like I did with warrock then it should work fine. Although you would have to have some sort of "TopMost" feature in ure IDE they have with VB.net. Err, I think there are other ways to tab down a window, I'll try using shell command and crap like that, I'll try I guess there nothing else for me to do.
*edit*
Fux minimizing the window is impossible. There is no fuxing way it can be done. You have a couple of options. Run the game so it thinks its maximized or run all hacking applets on top of the game.