Shades,
I don't think there's any easy built in way to do this with intensity graphs. There is however a way to do it that's a little challenging. It involves adding an offset to one of your data sets and setting a custom color range for your intensity graph. For one of your graphs add an offset that's greater than or equal to the largest intensity values in your other graph (making sure not to add this offset to the cells that have an intensity of zero). So lets say for example you had 2 2D arrays whos values ranged from 0-100. Lets call them arrays A and B. Add 100 to each value in array A (except when the array value is zero). Then add array A and array B (assuming they are the same dimensions). You then need to go into a loop and set the zscale.markervals[] property. Lets say we want array A to be blue in the plot and array B to be red. We want our array of clusters to look like the following...
0 black
1 very faint red
...
99 very dark red
100 black
101 very light blue
...
200 very dark blue
When all is said and done, you will have both of the plots on the same graph in different colors. You will just have to remember that if you want the numerical intensity of any of the offset plot's points you will have to subtract the offset first.
Hope this helps,
Justin D.
Applications Engineer
National Instruments