In your layout.master, find the <portal:LayoutPanel /> that is your Top Pane. Add SkinID="TopPane" to the portal, if it's not already there.
Next, in your theme.skin, add something like this:
<portal:LayoutPanel runat="server" SkinID="TopPane"
Element="div"
ExtraCssClasses="yourtoppaneclass"
/>
Next, in your CSS, add something like this:
.yourtoppaneclass .modulecontent { padding: 0; }
Hope this helps,
-Isaac