Change How the Network-Wide Ad Looks
From the “Settings > Extras” page you can set one of five places for the ad to show (should you be generous enough to actually enable the ad on your own site): above everything, above the header, below the header, between the main nav bar and the webcomic, and below everything.
We also have no problems with you using your own custom CSS (“Appearance > Edit CSS”) to style the area around the ad. We can give some CSS pointers if you need them. You can look at the source code (we recommend using Firebug or Chrome’s Developer Tools) to see the currently applied CSS. If you have questions regarding this, ask through the comments area below, our contact page, or the forum.