ManasviSihag, here you go:
for atmega 128 arduino bootloader check this out:
http://arduinoexplained.blogspot.ca/2012/03/how-arduino-download-programs-to-board.html
http://arduinoexplained.blogspot.com/2012/03/custom-board-programming-on-arduino-10.html
its a big tricky business (for me as i am not an expert programmer 
) but i think its doable XD
good luck