Yes, there are two ICSP interfaces[ICSP and ICSP1]. But, the ICSP1 interface is connected to the Atmega16 U2-MU. I think this unit handles the USB interface as is evident from the schematic http://arduino.cc/en/uploads/Main/arduino-mega2560_R3-schematic.pdf. Usin the ICSP1 interface, we cannot modify the fuses of Atmega2560 16AU. Please correct me if I am wrong ?