I've just made an application that will make using the NDS touch screen with arduino a lot easier. It has a rectangle the exact same size as an NDS touch screen. Basicly, you draw a rectangle using the mouse onto this area, and it creates some arduino code that will execute when you press the touchscreen in this area. You can also save the design of the touchscreen, so you can print it off glue/stick it behind the screen when your using it. The only thing is, I'm not sure if it works because I'm still waiting for a breakout board, but in theory it works, I've used some of the code written here and just made the software work out the coordinates relative to the screen.
You can download it at: http://code.google.com/p/touchscreen4adruino/downloads/list