If you want to customize the YITH WooCommerce Email Templates templates, you should copy and paste them into YOUR_THEME_FOLDER/yith-woocommerce-email-templates/emails/
Example 1
If you want to override the email-order-details.php template, you should copy the yith-woocommerce-email-templates-premium/templates/emails/woocommerce3.2/emails/email-order-details.php file and paste it into
YOUR_THEME_FOLDER/yith-woocommerce-email-templates/emails/ folder
Example 2
If you want to override the email-header.php template, you should copy the yith-woocommerce-email-templates-premium/templates/emails/woocommerce2.5/emails/email-header.php file and paste it into
YOUR_THEME_FOLDER/yith-woocommerce-email-templates/emails/ folder