You can change the plot of a cursor programmatically very easily. I assume you are programming in CVI since you posted to the CVI forum. Using the CVI generated instrument driver for the CWGraph, you would change the plot of the cursor with this code:
/Set up the new cursor to snap to Plot 1
CWUIControlsLib__DCWGraphGetPlots (hCWGraph, NULL, &hPlots);
CWUIControlsLib_CWPlotsItem (hPlots, NULL, CA_VariantInt(1), &hCurrentPlot);
CWUIControlsLib_CWCursorSetByRefPlot (hCurrentCursor, NULL, &hCurrentPlot);
You could change to any plot index you want to use.
Best Regards,
Chris Matthews
National Instruments