I see what you are thinking. To be honest those opening on your vehicle serve no purpose but for looks alone and create additional drag on your vehicle.
You can do three things with those holes:
1.) Close them off and try your best to fit the curve of your vehicle.
2.) Catch the air and route it to your brakes.
3.) Leave it.
http://electriccarsreport.com/wp-con...-Drayson_5.jpg
As you see in this picture they are routing the air around the tire at a nice steep angle.