Freaduino MEGA2560 is an Arduino compatible board. It is based on Arduino MEGA2560 design. So you can use Freaduino as Arduino MEGA2560. All code, shield and IDE for Arduino MEGA2560 are also valid on Freaduino MEGA2560. Some visible improvement on hardware make Freaduino MEGA2560 more flexible and easier to use. For example: 3.3v or 5v IO selectable allow you connect some 3.3v modules (such as XBee) to Freaduino MEGA2560 directly.