Avr Studio

Can I program the Arduino using the bootloader and thus the USB port in Avr Studio?

I’m not sure, but if you can, you’ll need to tell avr studio that you’re using a stk500 (version 1) device at 19200 baud. And an ATmega168.

well i can create the hex file in avr studio, just wondering how i’d go about up loading it that way, there must be a commant line command at least! (im using win xp)

You can use avrdude.