The window of ATC by default is quite large.  Although it can be resized and repositioned as desired and remains applicable during the flight-simming period, it will revert back to the default situation when FSX is exit.

To change the default size and position of ATC permanently:

1. Open the default flight (or any flight) in FSX
2. Activate ATC
3. Resize and reposition the ATC window as desired
4. Save the flight as default again
5. Restart FSX

The ATC window will start with the new size and position just defined from now on.