Due AT91SAM3X8E timers and corresponding registers: Names and how to access?

I’m trying to modify the timers on my Due AT91SAM3X8E processor like in this article: http://arduino.cc/en/Tutorial/SecretsOfArduinoPWM

Basically, I need to know the equivalent for the ARM processor of:

#include <avr/interrupt.h>
TCCR2A = _BV(COM2A1) | _BV(COM2B1) | _BV(WGM21) | _BV(WGM20);
TCCR2B = _BV(CS22);
OCR2A = 180;
OCR2B = 50;

What the corresponding timers and registers are for the Due ARM processor?

And what would be the correct library to include to access these registers so I can modify their bits?

You should be able to find all that in the datasheet:

AT91SAM ARM-based Flash MCU SAM3X SAM3A Series http://www.atmel.com/Images/doc11057.pdf

You'll probably have to look in the Arduino DUE core sources to see how "analogWrite()" is implemented if you want to change how it is implemented.