According to the SAM3X handbook it can do debouncing of interrupts "automatically", how would I enable that on an arduino due? The doc http://www.atmel.com/Images/doc11057.pdf states something about setting it directly in the PIO.
You can search the datasheet for "ebounc", which matches various spellings of "debouncing" related words. Especially chapter 32.5.9 in the datasheet you refer to describes "Input Glitch and Debouncing Filters". Find the registers that match the debouncing configuration for the I/O pins you need.
This Arduino forum post talks about direct register manipulation. In this respect the Arduino IDE works identical to how you program it in 'bare' C.