You can do this in one of two ways, depending on the version of NI-DAQ you are using. If you are using 7.2 or later, you can use the counter write functions (ex: DAQmxWriteCtrFreq()), which are available for each flavor of pulse generation tasks (Freq, Time, Ticks). If you are using NI-DAQ 7.0 or 7.1, you can modify the attributes directly (DAQmx_CO_Pulse_HighTime, DAQmx_CO_Pulse_LowTime, etc). Keep in mind that for each attribute pair, one of the attributes will cause the counter to load the new pair. The attribute that causes the load is LowTime, LowTicks, and Frequency.
I hope this helps!
gus....