The product isn't one of ours, and the datasheet doesn't completely characterize the encoders, so take this as an educated guess:
The datasheet shows two encoder channels and mentions a Hall effect sensor, so I'm going to assume the signals are digital and run in quadrature.. signal A goes HIGH before signal B if the shaft is rotating clockwise, B arrives before A if the shaft is rotating counterclockwise. That's a standard motor sensing approach.
If those guesses are correct, you don't need to use the ADC at all. You just need to count digital pulses coming from the A and B lines, and 90kHz won't push the limits of an 8MHz or 16MHz microcontroller.
The usual solution would be to set up interrupts for two pins so they can sense when the A and B lines go HIGH or LOW. Each pin's interrupt handler would find the state of the signal it observes, then store that information to a global variable you can use in the rest of your code.
The motor's direction and speed can be derived from the quadrature signal, and from those you can calcualate displacement from an originally recorded position. The details of how much work to do in the interrupt handlers and how much to do in the main code will depend on the requirements of your application in general.
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