This thread, particularly the first message with a schematic, may help you; http://arduino.cc/forum/index.php/topic,80483.0.html
Pay attention to the part labeled FTDI in the shematic, that should correspond to the USB to Serial adapter you have, wire the correct pins as shown in the above schematic. You will need to install a hardware core on your computer for this chip. Instructions for that should have come with you ATMEGA644 with bootloader, if not you MIGHT be able to use the core described in the above thread, which contains instructions on how to install.
After installing the core, you will either find your chip listed, or if you have to use the above referenced core, you will need to modify the boards.txt file for your chip.
Personally, I would contact whomever sold you the 644 chip and see what they can provide as far as instructions and core files.