Hello,
1) You are using WordPress and it is created by php files instead of simple HTML, so contact the plugin author and make clear in what area you need to add your code if you use WP.
2) Explain in more details about categories in the menu? Don’t you see them in backend or frontend?
Have you followed instructions to add your categories to menu https://docs.woocommerce.com/document/docs-menus/ ?
Regards