'Thank you' emails let your customer know you have received payment once you have marked invoices as paid within your accounting package. You can access your 'thank you' email templates under your credit control settings.
You'll find three templates, one for if the invoice is paid early or on time, saying thank you very much for the timely payment of this invoice. There is another template for non-timely payments. And finally, a grouped 'thank you' template. This is for where multiple invoices have been marked as paid on the same day for your customer. The grouped template puts the paid invoices into a table, you can amend these templates to suit your business needs, also.