Making the intercooler flush with the airdam would probably be best. Vents into the wheelwells will also help some. You'll notice most new cars have them.
For good aerodynamics, it's a good rule of thumb that it's better to have air move around the car rather than through it.
My suggestion would be to build a kammback on the rear at about a 10* downward angle, and have the end line up with the end of the tail lights. That should help control the wake a bit and reduce drag.
Something along the lines of this:
