Default logo according to theme setting
I think you can by adding algorythm like this:

&lt;div id="logo"&gt;
  &lt;a href="&lt;? print $front_page; ?&gt;"&gt;&lt;img src="&lt;? if (theme_get_setting(theme)=="dark") print $logo; else print $logo_light; ?&gt; border="0" alt="&lt;? print $site_name; ?&gt;"&gt;&lt;/a&gt;
&lt;/div&gt;