I found an example that does exactly what you need by going to zone.ni.com, and then searching for "counter and fly". This search pulled up an example with the following description:
This example is a Pulse Width Modulator in LabVIEW, which allows you to change the frequency and the duty cycle of a TTL pulse train generated on a Counter with out reconfiguring the board (on the fly). This VI takes advantage of the NI-TIO chip on the PCI-6602 board, but also works on the E-Series boards using the DAQ-STC chip. The subVIs that are included are modified versions of the DAQ 6.5.1 counter VIs. They are modified to acount for adjacent counters with the NI-TIO chip. When using an E-Series board and low frequencies, you are restricted to changing the pulse specific ations only once during a given cycle.
The URL to the example is attached below. I hope this helps with your application!