Arduino Due and tone()

Hardware Arduino Due
5

I'll answer my own question:
In order to get your square wave out on TIOA you have to set the appropriate bits on the TC Channel Mode Register:

  TC_Configure(chTC, chNo,
	       TC_CMR_TCCLKS_TIMER_CLOCK4 |
	       TC_CMR_WAVE |         // Waveform mode
	       TC_CMR_WAVSEL_UP_RC | // Counter running up and reset when equals to RC
	       TC_CMR_ACPA_SET |     // RA compare sets TIOA
	       TC_CMR_ACPC_CLEAR );  // RC compare clears TIOA

This solution is much accurate than using interrupts but it has the drawback that you have to use the pin associated with the TIOA0 signal (on arduino DUE this is pin 2).

Best regards,
Dan.