You should load the overlay twice, and adjust each layer indecently. The Scripting/templates/basic_paint_surface provides a Python script to illustrate this. In that example, the statistical map "motor_4t95vol" is loaded twice, once where the intensity range is -1..-2 with a blue-green color scheme and once with a threshold of 2..12 with the red-yellow color scheme. 

You can load overlays either with a script or the user interface. In both cases, multiple layers are shown in the "Overlays" panel, as shown in the attached figure: