There are two invoices - in fact they are the same but used separately. One is used only on the site after the purchase is made and the second one is used in the e-mail template. Their locations are following:
1) CMS Desk -> Tools -> E-commerce -> Configuration tab -> Invoice (devnet.kentico.com/docs/ecommerceguide/invoice.htm)
2) Site Manager -> Development -> E-mail templates -> E-commerce - Order notification to customer template