I am a little unclear as to what you mean by the phrase "signal the beginning and end of sampling". Do you mean that you want a signal from the IPAQ to trigger the sampling? Also, what measurements are you trying to "synchronize"? This will really hinge on what USB DAQ device you are referring to. There are E-series DAQ Pads, USB-6008/9, etc... Each of these has different triggering capabilities. Can you clarify your objective a little more?
National Instruments Applications Engineer