In .../variants/due/variant.* is a big array:
extern const PinDescription g_APinDescription[]=
{
// 0 .. 53 - Digital pins
// ----------------------
// 0/1 - UART (Serial)
{ PIOA, PIO_PA8A_URXD, ID_PIOA, PIO_PERIPH_A, PIO_DEFAULT, PIN_ATTR_DIGITAL, NO_ADC, NO_ADC, NOT_ON_PWM, NOT_ON_TIMER }, // URXD
{ PIOA, PIO_PA9A_UTXD, ID_PIOA, PIO_PERIPH_A, PIO_DEFAULT, PIN_ATTR_DIGITAL, NO_ADC, NO_ADC, NOT_ON_PWM, NOT_ON_TIMER }, // UTXD
// 2
{ PIOB, PIO_PB25B_TIOA0, ID_PIOB, PIO_PERIPH_B, PIO_DEFAULT, (PIN_ATTR_DIGITAL|PIN_ATTR_TIMER), NO_ADC, NO_ADC, NOT_ON_PWM, TC0_CHA0 }, // TIOA0
{ PIOC, PIO_PC28B_TIOA7, ID_PIOC, PIO_PERIPH_B, PIO_DEFAULT, (PIN_ATTR_DIGITAL|PIN_ATTR_TIMER), NO_ADC, NO_ADC, NOT_ON_PWM, TC2_CHA7 }, // TIOA7
{ PIOC, PIO_PC26B_TIOB6, ID_PIOC, PIO_PERIPH_B, PIO_DEFAULT, (PIN_ATTR_DIGITAL|PIN_ATTR_TIMER), NO_ADC, NO_ADC, NOT_ON_PWM, TC2_CHB6 }, // TIOB6
:
Add entries for your newly implemented pin(s).
Perhaps be careful about the "group" pins for entries greater than PINS_COUNT
(It doesn't look like anything error-checks against PINS_COUNT, and the array currently goes up to pin 91, so if all you want to do is GPIO, you can probably pretty much add the new pin to the end.)