Using the Hardware Quadrature Encoder Channel on the DUE

After an hour studying the SAM3X manual, I am getting a vague idea of how the decoding works - but can an example of how to also count the index be added to the working code example?

I am trying with an interrupt for the index, but the counts are low and drop more when the encoder is spun faster (TS5303 - can handle 5000RPM, pulses dropped at perhaps 100RPM).

I'm using 4N35s - perhaps they aren't switching fast enough?

Last question : the count keeps increasing, does it eventually overflow? can it be reset (per rev)? how is this normally handled?

I would be very appreciative of help here