By default your site will use the logo that you upload for your account. If you would like to add a different logo for each of your sites you can follow these directions.
Open the site template editor
To learn how to open the site template editor refer to the following article: How to edit your site design
Upload new logo
When uploading a logo it will be resized to fit within a 280x60 rectangle. You can upload a PNG, JPEG, or GIF image.