After a lot of searching i was finally able to upload hex files to Arduino mega2560 with the help of this small softwarehttp://www.ngcoders.com/downloads/arduino-hex-uploader-and-programmer
this software was only for m8, m168, m328p and m128
but the usefull thing about it was, it lets u change the command line for avrdude
so all i did was
>Replace the (avrdude.conf) in the software with the (avrdude.conf) that is in arduino-0022\hardware\tools\avr\etc\avrdude.conf
>Run the software and add the hex file
> Choose your com port and any microntroller i.e m328p
>Change the AVR Dude Params to:-
-F -v -patmega2560 -cstk500v2 -P\\.\COM24 -b115200 -D -Uflash:w:"your_hex_file path.hex":i
Don't forget to change COM24 to your COM port number
>Click the upload button and I WAS DONE!
If you guys have better way to upload hex file to meg2560 please enlighten me..