If you are programming in LabVIEW, you can use the Configure PWM Output VI to set up the frequency of the pulse train. If you are in any other language, you can use the NI-Motion API and call the flex_configure_pwm_output function to achieve the same result. Please refer to the NI-Motion C reference help that gets installed with the NI-Motion 6.0 driver or follow this link:
http://digital.ni.com/manuals.nsf/websearch/92003B670CC3CB3F862567C800755B95?OpenDocument&node=132090_US
for more information on this function.