1) The reference levels do not apply to the Voltage Average scalar measurement, so you don't need to set these. (They apply to rise time, fall time, width negative, width positive, duty cycle positive, and duty cycle negative measurements.)
2) Clearing the waveform measurement statistics will not affect the Voltage Average measurement itself. The driver can give you back not only the scalar measurements, but also statistics about those scalar measurements. When you call niScope Clear Waveform Measurement Stats.vi, it will reset the statistics, but will not affect the actual measurement that you are making. For example, say you fetched the Voltage Average scalar measurement four times, without clearing the statistics...
Voltage Average Mean (a statistic of the measurements)
+1 +1
-1 0
+1 .33333
-1 0
If you cleared the statistics after each measurement fetch, you would see this...
Voltage Average Mean (a statistic of the measurements)
+1 +1
-1 -1
+1 +1
-1 -1
since the statistics get reset every time.
To make a long story short, if you are only interested in the scalar measurement itself (Voltage Average, in this case), you don't need to call niScope Clear Waveform Measurement Stats.vi after each measurement.