Arduino Due with Atmel SAM-ICE for debugging in Atmel studio 6

Ok I am wondering if anyone has tried to debug a Arduino project with atmel studio 6 and got it to work. I have got an arduino sketch to work with the arduino plug-in but thats not what I am wanting. I want to get a arduino sketch, with whatever header files i need or what have you, working on the due where i can debug it using the Atmel Sam-ice. If anyone has any experience what so ever it would be greatly appriceated.

I love the Arduino IDE for smaller projects but i would love to get the due running (with arduino sketches) where they can be debuged over jtag..... i have everything i need but i guess i dont have the right header files and what not.