Bossac is not only a boot-loader tool for the SAM3X8E but supports all of Atmel's known flash-based SAM devices. I believe bossac checks automatically the CIDR of the MCU. Just try:
bossac.exe --port=COM1 -U true -i
I used comm. port 1 as an example. Remember to change to your current COM port.
Also change to 'false' if your are connecting to the USB-to-TTL serial chip.
You should program your sam3x8c using bossac in the same way you do it for Arduino Due.
Anyway, I have a 3x8c system at home and I can try some tests tonight.
<< Do not use the Arduino IDE to compile/program your SAM3X8C based board at least you have the variant files redefined for the 100-pin package of SAM3X8c. I am not sure about the uart interface settings but may be you will need to redefine them too.
I would recommend you to use Atmel Studio 6.1 where you can create bare minimum project templates for the SAM3X8C which will automatically generates the 100-in/out pins and other utily files. Just let me know where you are in your project (stage).
You can always count with the at91 Atmel tech support team after generate a ticket. >>