What should O2 ref be set to?
O2 ref only needs to be set when a consent limit has been set by a controlling authority for the emission of a particular toxic gas. This ensures that all the readings are normalised and cannot be manipulated by adjusting the level of excess air (ie diluting the sample).
Typically authorities require the measured sample to be referenced to 3% or 5% oxygen.
See also What does COn mean? and What is air free CO?