I use a label as placeholder for a banner, lblBanner, on top of my layout.
Then, all other views below it; maybe the best thing is to place a panel big as the rest of the space.
I "draw" my layout, adding views and setting their anchors.
Then I must add the script to resize the height of the banner (lblBanner) and I must change the top position and the height of the "base panel", loosing what anchors did.
Are you setting the ad size to SIZE_SMART_BANNER? If not then the height will always be 50dip.
Assuming that you are adding a smart banner then it will be simpler to add it in your code, add a panel beneath it and then load the layout to that panel (without a placeholder for the banner).