The Woocommerce team strongly suggest you modify your theme with add on files rather than edit the plugin. This process makes your work much more 'upgrade proof'
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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.