How to upload a hex file to arduno in windows?

How to upload a hex file to arduno in windows? I am trying to use the bootloader and usb cable to program the mega 168 on the arduino board in windows. I program with winavr.

You can’t program the bootloader through USB, afaik.

You will need a special programmer to do this, for example this one: http://www.arduino.cc/en/Hacking/ParallelProgrammer

You can't burn the bootloader via USB. If, however, you've got a chip with the bootloader on it already, you can upload a .hex file with USB. You'll want to use avrdude, at 19200 baud with stk500v1, and you may need the -F flag too.