Themes

 In your theme header.htm file you have the following line (line 33 on mine) that is calling in logo.jpg. You could change the name of the image here and assumedly add a second similar line to call a second logo. You can then apply the necessary styles through your CSS file using classes or ids as necessary. You may also want to add smaller versions of the logos further down  (line 39) for non home page headers.

<div class="headermain"><img src='<?php echo "$CFG->wwwroot/theme/$CFG->theme" ?>/logo.jpg' alt="eCampus Logo"/></div>