I ended up only going with partial rear wheel skirts on my Civic in combination with smooth wheel covers. Bending the material to clear the wheels made it stick out and slightly reduced gas mileage. My best prototype rubbed against the wheels, which I removed. Combined with smooth wheel covers, the partial rear wheel skirt that I did provided most of the benefits of a rear wheel skirt. Just a thought in case you have trouble clearing the wheels with your skirts.
EDIT: Continuing the skirts down lower and combining them with rear wheel spats might've helped even more, but I didn't get that far in ecomodding with the car.
