Yes, you will still gain from the skirts even with the pans on your wheels. The pans may be flat, but they're still moving. And the tires aren't all that flat on the sides, so they'll all still be grabbing air and throwing it around. With the skirts in place, there will be less air for them to grab.
(Yes, that's an immense oversimplification. But it gets the idea across.)
-soD
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