Reading 2 Quadrature encoders using a single Arduino Due
If the encoder frequency is not too high it's just a matter of keeping track of the count using an up-down counter and two general purpose input pins.







simulate this circuit &ndash; Schematic created using CircuitLab

Figure 1. 2-bit rotary encoder waveforms.

The program logic is very simple. 


Track the current state of 'A'. If the state changes to 'high' then:
Look at input 'B'. If 'B' is low then count up. If 'B' is high then count down.


You'll probably need to debounce the inputs to prevent spurious triggering. You then need to write some code to detect the rising edge of the 'A' pulse.