I am studying the block diagram and the pinout of the ATSAM3X8E (http://www.atmel.com/Images/Atmel-11057-32-bit-Cortex-M3-Microcontroller-SAM3X-SAM3A_Datasheet.pdf) of the Arduino Due board, but I am a bit confused. How do the pins match to the I/Os of the block diagram?
You can find all the information you need in the Greynomad pinaout diagram :
That's a pretty awful "block diagram"; the Arduino mostly treats pins as GPIO, which shows up in the block diagram as little blocks (PIOA, PIOB, PIOC) in the upper left-hand corner, not connected to anything. Sigh.