+In the Overlay plugin's parameter window you can choose the overlay "Layer order"
+to select which track plays the role of the "bottom layer" and which plays the
+role of the "top layer". For some overlay modes this can make quite a
+difference, for example the bottom layer is subtracted from the top layer for
+"Subtract" mode. Also in the parameter window, you can choose on which of the tracks
+to overlay the combined output by changing the "Output layer" and it too can make
+quite a difference.
+(Hint: in most cases, you will want to mute the other track so you only see the
+combined output).
+