Click the 'Print postage labels or invoices' link from an order.
On the next page, cick the 'Edit invoice and address label template' link.
The option to include a logo is there. I couldn't get the "use store logo" option to work. The option to pull it from a URL works, but keep in mind the invoicing template is ancient, and the image dimensions are based on the old store logo format, which was rectangle, not the new square format. You want an image that's around 310 (w) x 90 (h), or maintains an aspect ratio about that size, so 620 x 180, and so on, as otherwise it will get stretched out to fit the rectangle.
