We typically recommend choosing a motor controller that has a continuous current rating equal to or greater than your motor’s stall current. For example, if the starting current you mentioned is the stall current, you might consider the RoboClaw 2x45A. If the stall current of your motor is higher than 45A, you could consider the RoboClaw 2x60A instead.
It looks like that encoder can output pulses as low as 2.4V. The RoboClaw is intended for use with 5V encoders; I am not sure what the minimum voltage is for the RoboClaw to detect the signal. You might contact the manufacturer, Ion Motion Control, to see if they can confirm if it will work.
You can control the two motor channels on the RoboClaw controllers independently, so it is fine to control a single motor driven from one channel of the RoboClaw without using the other channel.