Tab: Marketing > Website (the Business: Website tab). Three file settings (global only):

• Company Logo – the main logo used in the site header, emails, the order view (when Show Logo is set to Client Logo), and the post-registration welcome popup.
• Company Logo Footer – an alternative logo for the site footer; when empty, the footer shows your Company Name as bold text instead (it does not fall back to the main logo).
• Company Favicon – the browser-tab icon, Apple touch icon and web-app manifest icon. Upload a square image (PNG recommended).

Choose the file in the row's file input; it uploads immediately (the form submits itself on file selection). Use the red X next to an uploaded file to remove it and return to the default.