It's gonna be a tough one - I assume you mean changing the width of the top 2 or so posts so the banner fits beside them then leave the rest at the full width. You'd need to edit IPB's PHP scripts to generate (for instance) the cell with the advert with rowspan="2" then all but the top 2 posts with colspan="2" (as attributes).
The problem with that is it varies a lot depending on the exact posts, screen size and so forth so it could get very messy very quickly. It's also hard to explain, the first sentence makes that pretty clear.