I think you have to install Atmel Drivers to recognize the "native" port; I don't think it appears as a COM port. (at least, not if you're relying on the original ROM'ed bootloader. After you upload a sketch, the serial port may appear.)
I did try to install SAM BA driver...and also SAM BA CDC .inf file.
but dont know how to use them. as in how to get them installed.
since them I am trying to understand bossa but not understanding its implementation in clear simple steps.
coming to your suggestion, if i dont have a com port , how do i upload int the first place.
The SAM3X has a built-in bootloader. I'm not sure what steps you need to take to use it; unlike the Arduino bootloader, vendor bootloaders tend not to run unless you specifically request it. This may involve the mysterious "erase" button.