Magento has a strange way of rendering configurable options on a product page. Basically, when you create a configurable product, you have the option of selecting whether the options fall in container1 or container2 (great naming, eh?) You can adjust this in the product edit screen under Design > Display Product Options In.
However, a much easier solution is to move container2 above container1 in your catalog/product/view.phtml
file as all configurable products default to Block After Info Column.
This is the code you're looking to move if you're using CE:
<?php if ($_product->isSaleable() && $this->hasOptions()):?>
<?php echo $this->getChildChildHtml('container2', '', true, true) ?>
<?php endif;?>