Subtracting elements doesn't appear to do much until you hide the layer that the operators are on (or switch it to wireframe display). More obvious is to use the subtraction with upwards or downwards extrusion (which I think should just be called "Subtract Up" and "Subtract Down" - that dialog is way too big). You will notice that SEOs create the intersection lines between elements in any operation and these are visible regardless of the layer settings.
As Ben points out the results are only visible in 3D. And, per Stuart, do not delete the operators or the effect disappears with them.