Template structure & Overriding templates via a theme
WooCommerce template files contain the markup and template structure for the frontend and HTML emails of your store.
When you open these files, you will notice they all contain hooks that allow you to add/move content without needing to edit template files themselves. This method protects against upgrade issues, as the template files can be left completely untouched.
Copy the template into a directory within your theme named /woocommerce keeping the same file structure but removing the /templates/ subdirectory.
Example: To override the admin order notification, copy: wp-content/plugins/woocommerce/templates/emails/admin-new-order.php to wp-content/themes/yourtheme/woocommerce/emails/admin-new-order.php
The copied file will now override the WooCommerce default template file.
If you are a theme developer or using a theme with custom templates, you must declare WooCommerce theme support using the add_theme_support function. See Declaring WooCommerce Support in Themes at GitHub.
If your theme has a woocommerce.php file, you will be unable to override the woocommerce/archive-product.php custom template in your theme, as woocommerce.php has priority over other template files. This is intended to prevent display issues.