In a previous message you stated that you have phase a +/-, phase b +/- and phase c +/- outputs - now you mention a phase d output???
Unfortunately encoder manufacturers use different designators for the encoder index output. Some call it I, others Z, maybe the C output(s) is the index signal in your case. You can check this by monitoring the encoder as you turn the motor (the encoder must have a power supply, see below). The index signal should occur only once per revolution - but usually for a very short time only, you will need a scope set to single trigger.
However, since you obviously have differential output signals, you first have to 'translate' them to single-ended TTL signals as they can be processed by NI motion controllers. This can be done with an Am26LS32 ic. The connect the (translated) phase A signal to encoder A pin, the phase B signal to encoder B and the encoder signal C to encoder index. An index signal is not absolutely necessary to run a motor with feedback.
Your encoder probably needs a power supply. Most encoders run on 5VDC, and you may use the +5V output of the NI controllers as long as you do not exceed maximum load of 100mA.
Concerning the control pins, your driver seems to use differential signals for CW/CCW inputs, too. The NI motor controllers can be set up for both step/direction or CW/CCW signals. However, they will only deliver TTL compatible output signals. They must also be 'translated' into differential signals by differential driver ICs such as the Am26LS31.
