So I will admit that I am a noob to Arduino. I have some experience programming microcontrollers, and that was back in the day (about 4 years ago - such as the Freescale 68HC12) so up until this point I thought I was experienced enough to get this Arduino Mega2560 rocking with AVR C using Atmel Studio and avrdude by lunch...
Wrong.
I believe I'm getting held up at what's possible...
What I want to accomplish: Write and compile a program in AVR C within Atmel studio. Use the hex file that was built and download that to the Mega. (Keep in mind I was planning on using USB and Arduino as my programmer between PC and ATMega2560 as per this gentleman's example... https://balau82.wordpress.com/2011/03/29/programming-arduino-uno-in-pure-c/ -- however, I was not using his code and he was compiling using avr-gcc...)
Question: Is this possible?
Using avrdude when attempting to write the file I get this message... (and my blinking LED goes dark for a few seconds before returning to normal operation)

When I searched the internet for this issue it was never related to avrdude, but rather a communications issue. I've verified my bootloader is still ok (uploaded other sketches with no issues).
It's certain that I am missing something minor, but this is my first day using Arduino so go easy on me!
Thanks