To add a link to the PDF invoice / receipt to your message templates, just use the %pdf% code in a message template. It will be replaced with a link to the PDF itself, in the message's body. Note that this will not add the PDF file as an attachment to the message, but a hyperlink that leads to the PDF on your website. Attaching the PDF is not available right now, but will be coming in a future version of WP-Invoice.
Please, note, that any code customizations you make on your own risk. We won’t debug your templates if they look bad or cause issues.