How to use all pins on SAM3X8 ?

Hi there guys im just in the process of designing a new PCB using the SAM3X8 witch will have a 3.2" touch display built in and lots of extras that the DUE dose not have. I have been reading up on the Pin mapping of the chip there are a lot of pins on the chip that where not used on the DUE That I would like to use But can I ? is the thing. These the the pins not used ON THE due PA5, PB28, PB29, PB30 ,PB31 PC11, PB0, PB1, PB2, PC10, PB3, PB4, PB5, PB6, PB7, PB8, PB9, PC0, PC20, PC27, PB22, PB23, PB24, how can I use them as outputs do I need to change files to use them?

Hi, I have bought a board developed by others. It seems that we can use all pins on the board. My board is not arrived yet.
Recently they are raising fund:

You can see here. After my test, lets discuss more.

do I need to change files to use them?

Yes, I think the PinDescription array in variant.cpp is the place to start.