counting pulses using digital input channels on 6289

I am using PCI 6289 card. where 2 counter ctr0 and ctr1 are already being used for stepper motor driver. Now we want to read the position of the stepper motor using installed rotatory  encoder at the same time or in real time. Can we use digital input channels available or any method other then counter input, to read the position of the encoder/stepper motor.

NI PCI 6289

LabVIEW 2014