Layout on Commerce checkout pages
You can get at that with the commerce functions hook_commerce_checkout_page_info() and hook_commerce_checkout_pane_info(); with more documentation on that here: http://www.drupalcommerce.org/developer-guide/core-architecture/info-hooks/checkout-info-hooks#checkout-pane.

It's a little complicated because the panes, pages, and forms are hard-coded into DC's checkout logic. There are a couple of modules that let you override and specify your own pages or other cart functions https://drupal.org/project/dc_co_pages, and https://drupal.org/project/commerce_cart_view_override

You'll probably need to do any serious changing by coding your own module calling the commerce functions/pages you need for your use case.