the wax is applied last - if you look in the wheel well - you will find a few holes with rubber covers on them, those holes were specifically drilled to apply the wax coating. The largest one near the front edge opens into the "footboard' aka sill aka rocker panel. wax is applied liberally there too.
Dont confuse undercoating with wax, btw the undercoating extends out all the way till the lower edge of the footboard or sill panel to protect against rusting.
When installing the tail lamps back - make sure that the foam rubber gasket is good - if its not then water gets into the boot and creates a nasty muggy atmosphere which also stinks and causes fungus and bacteria growth.