You find ${site_logo} in a file "init.ftl". This file is in: liferay-portal-src-6.2.0-ce-ga1\portal-web\docroot\html\themes_unstyled\templates\init.ftl
To change the src, include in init_custom.ftl #set ($company_logo_src = "$images_folder/yourlogo.png"). Then in your portal_normal the tag img put src="$company_logo_src"
$images_folder is going to take the logo from folder images (of your theme). This var exist in init.ftl and have this value $theme_display.getPathThemeImages()