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:
- Open the default flight (or any flight) in FSX
- Activate ATC
- Resize and reposition the ATC window as desired
- Save the flight as default again
- Restart FSX
The ATC window will start with the new size and position just defined from now on.