It shouldn't be necessary to modify emulator code. It might make things easier, but it wouldn't be the only way to do it. Server-side applications (that's the one on the PC, for those wondering) could have a "frame" system, for example. Place the frame over the lower screen on the emulator and mouse input will be confined to the frame instead of the whole screen. I'm sure there's other (better) ways to deal with it, but that's my first thought.