Directly from Woocommerce:
http://docs.woothemes.com/document/template-structure/
The template files of WooCommerce contain the markup and template
structure for the front-end (and HTML emails) of your store. If you
open these files you’ll notice they all contain many hooks which will
allow you to add / move content without having to edit the template
files themselves. This method protects even further against any
upgrade issues as the template files can be left completely untouched.Alternatively, you can edit these files in an upgrade safe way through
overrides. Simply copy it into a directory within your theme named
/woocommerce, keeping the same file structure.Example: To overide the admin order notification, copy:
woocommerce/templates/emails/admin-new-order.php to
yourtheme/woocommerce/emails/admin-new-order.php The copied file will
now override the WooCommerce default template file. Do not edit these
files within the core plugin itself as they are overwritten during the
upgrade process and any customisations will be lost.The template files can be found within the /woocommerce/templates/
directory.