I am assuming by multiple y-scales do you mean you have multiple traces on the xy graph and each one has a different scale. If that is so, you can change this by using the Active plot property node to cycle through all the traces on the xy graph.
You need to use the Active Y Scale property first. The Y scales are numbered with indices 0,1,2... You need to use the Active Y Scale property and wire the appropriate index for the Y scale you want to change, then set the property. That way the property will apply to whichever Y scale you indicated. See attached picture.
One of the problems with using two Y scales is that the display can get very messy is you also want grids on the plot. To address this, I created the attached VI. After allowing the right axis to autoscale, it fine tunes the marker locations so the grid lines for the left and right side overlay each other.
To use it all you have to do is write your data to the graph and then call this VI with a reference to the graph.
Mike...
Certified Professional Instructor Certified LabVIEW Architect LabVIEW Champion