Hi Matt
The first thing to do is to copy all the classic directories where you have changed code to new directories so that you are working from a copy of the classic template, rather than the classic template itself. Otherwise when you next upgrade, you will overwrite all your good work.
To achieve the dual logo, edit the common/tpl_header.php file in your template (making a copy of the one in template_default if you haven't previously altered this file).
The changes that you will make to it are relatively straightforward. You find this line> <div id="logo"><?php echo '<a href="' . HTTP_SERVER . DIR_WS_CATALOG . '">' . zen_image($template->get_template_dir(HEADER_LOGO_IMAGE, DIR_WS_TEMPLATE, $current_page_base,'images'). '/' . HEADER_LOGO_IMAGE, HEADER_ALT_TEXT) . '</a>'; ?></div>and then duplicate it changiong the id to logo2.
Then in your stylesheet.css you add> #logo2 {
float:right;
}