<div style="float: right; background-color: red; width: 400px; height: 60px; margin-top: 20px; margin-bottom: 40px;">
AD CODE HERE
</div>
Here is the result:
You can change the dimensions and margins as needed.
You may need to increase this setting to accommodate more vertical space in the header, otherwise you may notice that elements below the header are out of position:
Admin CP -> Appearance -> Style Properties -> Header and Navigation -> Height of Header Logo