Eried, I did some research for the hex upload with Avrdude and here is what I have found so far.
A program with source code for uploading Hex files: Arduino Playground - ArduinoUpload
Here is a thread that may give clues to the process: http://arduino.cc/forum/index.php/topic,37586.0.html
qoute from anther thread************************
Re: Upload Blink sketch using AVRDUDE command line
This is the comand line I've used:
avrdude.exe -V -F -C avrdude.conf -p atmega168 -c stk500v1 -P COM2 -b 57600 -U flash:w:Blink.cpp.hex -vvvv
I will be try to gather more information if you need it. Thanks for the efforts.