In order to make your custom template, please copy the default template files (including folder) you’ll find in:

 plugins/woocommerce-pdf-invoices/includes/templates/invoice/simple 
to
 uploads/woocommerce-pdf-invoices/templates/invoice/simple 

The plugin will automatically detect the template and make it available for selection within the Template Settings. Now you should be able to start making changes to your files. 

Important: Before you update the plugin, always have a look at the Changelog if there have been any changes to the template files. There will be updates that require updating your custom template!

Keep in mind that the custom template has to have the same name as the template you’re replacing. If you want to generate credit notes and packing slips, you need to make custom templates for these too with the same name.