Well I had the same problem, I just finaly had to drill small holes through the skirt and the car (I know this sounds scary) but I alway plan on having a body kit on my car so the kit will always cover the holes, besides I want to eventually paint the car a different color and its easy to fill the holes if I want.
After you drill the holes, get some touch up paint and paint inside the holes on the car so it dosent rust over time, then secure the skirt to the body using small matal screws, use stainless steel so the screws dont rust. I know what your thinking, the skirts will look ghetto with screws heads poking out, right?
Well I have a solution for this also. go to home depot in the hardware section and you can get plastic screw covers, they look like little bubbles you can kinda see them in my pic. then you paint the screw covers to match your car and pop them on the head of the screw. I know this sounds like a lot of work but it only took me about an hour and when your done, no annoying gap and it is barely noticeable.
Well thats my 2 Cents...
Here is the pic look closely at the side skirts and you can see the caps.