How to override output of checkout page in Commerce
It looks like using hook_commerce_checkout_pane_info_alter(&amp;$checkout_panes) or hook_commerce_checkout_page_info_alter(&amp;$checkout_pages) would be the best options. There are also hooks that allow you to create your own checkout panes/pages from scratch if necessary (hook_commerce_checkout_pane_info() and hook_commerce_checkout_page_info()). I would suggest reading more about them here and checking out the specific examples (about page/pane info hook implementations) that you can find in the Drupal Commerce submodule (mostly Checkout) files.