I use AVRDUDE to programming this chip. You run AVRDUDE in a command prompt in Windows, and in a shell in Linux.
This is the command I used to upgrade to version 3.06 of the Ultimate 3 software. Obviously, you may find that you will need to change the COM port.
avrdude -p m328p -P com13 -c arduino -b 19200 -U flash:w:Ultimate3.06.hex -U eeprom:w:Ultimate3.06.eep -U lfuse:w:0xF7:m -U hfuse:w:0xD9:m -U efuse:w:0xFC:m -U lock:w:0xFF:m -U calibration:w:0xFFFFFFB9