To program a blank mega644 chip, use the following:
avrdude -c usbtiny -p m644 -B 250 -U lfuse:w:0xe2:m -U hfuse:w:0xd1:m -U efuse:w:0xfe:m
(in case avrdude complains the signature does not match, add a -F option to overwrite the signature checking)
Then you can flash a firmware with:
avrdude -c usbtiny -p m644 -U flash:w:firmware2.0.0.hex