I assume you're using stepper motors. In this case, your BEST solution is to use an NI motion control card (NI-7334 or NI-7344). However, if you'd like to use the PC-1200, it should work, but it will depend on your motor amplifier.
Usually stepper motor amplifiers take two inputs: step and direction. In this case, you would use the Counter output of the PC-1200 card for step and a DIO line for direction. If the amplifier has an input for clockwise motion and another input for counter-clockwise motion, then you'll need to use two of the counter outputs on the PC-1200.
NI-DAQ 6.9.x ships with many example programs that should show you how to create a pulse train from the DAQ board