To update the branding used on your invoice template you can upload your company logo under the "Business Profile" menu option in the top-right settings menu. That logo will appear on the documents you send to each of your clients. In addition, you can change the header color on your invoices. To do this:
Start with the invoice you wish to send.
Click "Send" on that invoice
Toggle the "Edit Template" radio button
Choose from a preset color or enter your own custom hex color value
It's as easy as that. From then on, all invoices will follow this template. Just set it and forget it!