If you are AVRDUDE savy, you can use the README.txt in \hardware\arduino\firmwares:
avrdude -p at90usb82 -F -P usb -c avrispmkii -U flash:w:MEGA-dfu_and_usbserial_combined.hex -U lfuse:w:0xFF:m -U hfuse:w:0xD9:m -U efuse:w:0xF4:m -U lock:w:0x0F:m
Other than that, there is FLIP and the DFU tutorial:
Or use the AVR ONE! and burn the MEGA-dfu_and_usbserial_combined.hex file...