You can define the header and footer of the Thank You page by going to the Commerce Setup > Order System > Thank You Screen. You can use HT ML in the text fields, so you can add logos and customize the page in many ways. The colors that you set in the Commerce Setup > Order System > Layout Info screen apply to the shopping cart page, the shipping/billing page, the optional confirmation page, and the thank you page.
To completely customize the e-mail receipt and any other shopping cart pages, create a custom shopping cart template.