If you want to have a logo appear on all pages regardless of the journal, you'll need to modify the main header template (templates/common/header.tpl) or site-wide CSS file (styles/common.css). The template file is Smarty code, which you can generally modify as if it were standard HTML.
Open Journal Systems Team
Don't miss the First International PKP Scholarly Publishing Conference
July 11 - 13, 2007, Vancouver, BC, Canada