To upload a logo for the Invoices module, click on "Full Settings List" under the "Quick Links" tab.
The Settings page has a comprehensive listing of front-end settings, scroll down to Invoices and click on "Invoice Logo".
You'll be taken to the Invoice settings page where you can add a logo. Click on "Browse" to add a file from your computer. Be sure to select "Update Settings" after you've uploaded your logo.
The same logo will appear on all invoices and the logo will always crop to 300 x 150 pixels.