I think this is related with theme your using. I mean, if your theme does not provide it out of the box, then you have to edit the sidebar.php of your theme, so it can be devided one column at the top and two column at bottom. Not only that, you have to register additional widget areas for new added blocks. This requires a little bit of PHP programming and WordPress theme structure.
I can’t deep into details, but roughly the layout should be like the following HTML code:
<div id="outer">
<div id="top">
<!-- content for top block goes here -->
</div>
<div id="bottom">
<div style="float:left;width:50%">
<!-- content for bottom left block goes here -->
</div>
<div style="float:right;width:50%">
<!-- content for bottom right block goes here -->
</div>
</div>
</div>
If it helps i can recreate a theme that has 2 sidebars down the one side and then i would just have to do the opposite and close the top section up after