Hi there. It was a mystery for me as well. I am not a Command line person. So I used AVR Tools (http://www.w7ay.net/site/Applications/AVR Tools/), which is a GUI for AVRdude. You might need also to install Crosspack (link is there as well) So, in AVR Tools you need to select three things: Under Device select ATmega328P, under Programmer select Type: Arduino and proper Serial port. I added link to hex file in both Flash and EPROM fields. Hope it helps.
I just posted in troubleshooting I think about this subject. I am having trouble seeing the controller through the usb. I did the terminal 'stuff' it said to do but dont know anything about GUI (whatever that is) as Im very new to remote things ie week 2. Is your recent post what I have to do also?
Thank you Jigit. Unfortunately I have absolutely no knowledge of what is a GUI etc so I would love step by step instructions if someone has the time. It is all really confusing to me.