Guess if I monkey around with it enough...what I did was set the bounding rectangle for the view, to start at the bottom of the iAd banner, and subtract the banner height from the view height.
In the View Controller's viewDidAppear
method:
...
[self.view addSubview:theAppDelegate.adBanner];
CGRect mainViewFrame = CGRectMake(0, theAppDelegate.adBanner.bounds.size.height, myNavController.view.bounds.size.width, myNavController.view.bounds.size.height - theAppDelegate.adBanner.bounds.size.height);
[myNavController.view setFrame:mainViewFrame];
[self.view addSubview:myNavController.view];