Crown molding is strips of decorative wood and wainscoting is a type of paneling that you add to a wall, usually only placing it halfway up, to give a decorative flair to your room. It is installed by nailing or gluing the wainscot paneling to the wall in strips, and usually it is finished off with what is called a chair rail. However, when it comes to installing crown molding, which is strips of decorative wood trim, you could use that to finish it off, instead of a chair rail. You would be putting it on the top of the edge of the wainscoting, not on top of the wainscot panels themselves. Therefore, the answer is that you put it on the top of the wainscoting, not over it.