I don't think it matters too much where the actual map portion goes in the code. I've also put it below the footer on a zen cart site before. But you can hard code the logo so that you can add the usemap portion. So instead of this:
<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>
You'd do something like this:
<div id="logo"><a href="http://miss-crow.com/shop/"><img src="includes/templates/cherry_zen/images/logo.gif" alt="ALT TEXT HERE" width="999" height="336" usemap="#name_of_map_here" /></a></div>
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