Google aims to put the highest paying ads to the top, so generally the bottom two ads of a skyscraper would pay less but displaying more ads can also increase click through rates so it could even out in that way. Also if you are displaying more than one ad unit higher ad units will again usually pay more than ones lower down the page. If there is space I usually fill it with the extra ads, a good thing with a skyscraper is if someone scrolls down a page ads may still be visible without scrolling back.



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