As Janka, mentionned, just leave the chip in the Uzebox, it will use the onboard crystal. But unplug power and any cable from isp port.
Download the latest Arduino IDE: http://arduino.cc/en/Main/Software. When installing Arduino insure the virtual COM port USB driver is installed. I'm on Windows with a UNO so adjust accordingly.
Start Arduino, go to Files->Examples and open ArduinoISP. Then from Tools->Board select Arduino Uno, from Tools->Programmer select AVR ISP or Arduino as ISP. Access Tools->Serial Port and select a port (ex. COM3) which is needed for avrdude. For me COM3 did not work, but I had another one in the list, COM5 which worked.
Finally, press Files->Upload, to load ArduinoISP to Arduino Uno. This operation transforms Arduino Uno into an ISP programmer.
Next Wire from Aduino (UNO)->Uzebox EXT header:
Pin10: RESET
Pin11: MOSI
Pin12: MISO
Pin13: SCK
5V: VCC
GND: GND
Next run avrdude, use the same COM port as selected in the Arduino IDE:
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avrdude -P COM5 -b 19200 -c avrisp -p m644 –n
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avrdude: AVR device initialized and ready to accept instructions
Reading | ################################################## | 100% 0.07s
avrdude: Device signature = 0x1e9609
avrdude: safemode: Fuses OK
avrdude done. Thank you.
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avrdude -P COM5 -b 19200 -c avrisp -p m644 -U lfuse:w:0xD7:m -U hfuse:w:0xD2:m -U efuse:w:0xFF:m
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avrdude -P COM5 -b 19200 -c avrisp -p m644 -U flash:w:Bootloader_0_4_4.hex -U eeprom:w:eeprom.hex