How to customize the add-to-cart form using hook_form_alter?
You can use this snippet to customize the add to cart form:

/**
 * Implements hook_form_alter()
 */
function MYMODULE_form_alter(&amp;$form, &amp;$form_state, $form_id) {
  if (strpos($form_id, 'commerce_cart_add_to_cart_form_') === 0) {
    // Your form modifications go here.
  }
}


The $form_id changes based on the product that is in it, so you have to check for the string at the beginning of the $form_id variable.

You can theme it and/or change markup in the form like you would a regular form.