Or, like in some paint programs you are able to assign a 'foreground' and 'background' color to left and right mouse buttons and then just go from there. I agree with ccs that it would be great if the right mouse button could erase.
So as far as intuitive controls, perhaps information about the S/L/D keys could be integrated into that area of the desk somehow. Before I checked the controls, I was clicking on the save scene boxes with the mouse, to no avail, since that was how you interacting with everything else.
Without looking at any of the controls, I figured out all except for the Save/Load/Delete keys just from intuition. The realtime clock, the mouse cursors that activate depending on which section of the table you're looking at, mixing up the different grid sizes in one drawing, and representing saved scenes as boxes in the drawer. You've done a lot of interesting things here.
