put this in your 'Configure Header area' option
HTML Code:
%logo %pages %cats
<!-- To remove the ad altogether, start removing here... -->
<div style="position:absolute;top:20px;right:20px;width:728px;height:90px;background:#ddd;">
<!-- Put the ad code BELOW this (and remove the sample text if there is any) -->
728x90 ad code here. Edit Atahualpa Theme Options -> Style & Edit HEADER AREA -> Configure Header Area and put your code inside the DIV
<!-- Put the ad code ABOVE this -->
</div>
<!-- End removing the ad here -->
you can play with the position and height/width numbers