Is there a way of automatically sending measurement channel two to the lower plot?

If you are going to calculate parameters that are based on two impulse responses, it may be useful to display measurement channel 1 in the upper plot and measurement channel 2 in the lower plot.

To do this, first go to Measurement->Settings... and select 2 channel measurement as shown in the figure below.

Now go to Plot->Plot Type/Routing/Test…. In the example below, channel 1 is routed to the first plot while channel 2 is routed to the second plot.

This also applies if several measurements are opened using File->Open…, then channel 1 measurement will be displayed in the upper plot, the channel 2 measurements will be displayed in the lower plot.

Note: If the wrong measurement is plotted, you may change this from Measurement->Information... or from the Measurement Selection toolbar.