I would recommend looking into DAQmx triggering. You could set up one task to trigger off the other and use a trigger delay to time the pulses correctly.
There are many synchronization examples built into LabVIEW - these can be found under Help >> Find examples >> Hardware IO >> DAQmx
Hope this helps,
Can you describe what you are using to make your measurements? i.e. the platform (PCI, cRIO, PXI, etc) as well as what you might be using your counters for. Most boards should have at least two counters associated with them which can be shared with other boards. Off the top of my head, the only way that I can think of actually having the counter pulses occur within the digital pulse is to generate the digital pulse on whatever line you are using, and then use the trigger property node to pause the counter when the sampled digital line goes high or low. I am not sure what latency to expect in the system for this method, but it should work about as well as routing the internal counter. m