The default logo file, named bmclogo.gif, is located in the /resources/img/ folder on the mid tier server. First, move your company logo to the /resources/img/ folder. Then, use the Self Service Portal Configuration tool to modify the Application Portal - Interface to point to your logo. The logo definition is the first line of the entry.
<logo>resources/img/bmclogo.gif</logo>
For more information, see Changing the logo in the application portal.