The best practice for editing a Woocommerce theme is similar to WordPress as you should use Hooks and Filters when possible.
https://docs.woothemes.com/document/introduction-to-hooks-actions-and-filters/
But if you do need to edit a template Woocommerce outlines this on their website as well: https://docs.woothemes.com/document/template-structure/
You just need to make the template upgrade safe by copying the template to your theme in to a woocommerce folder.