this is the setting of the actual header.php

gistfile1.phtml

<?php
	    $seo_title = get_post_meta($post->ID, '_yoast_wpseo_title', true);
	    $seo_title = apply_filters('the_title', $seo_title);
	    if($seo_title == "") $seo_title = get_the_title();
	    ?>
        <title><?php if (!is_home()) { echo $seo_title; echo " - "; } echo str_replace("%s", "", get_bloginfo('name')); ?><?php # if (!is_home())
	        echo " ";
        #get_the_title();#wp_title(); ?></title>

Yoast's SEO hooks into the wp_title() function, so all you really need is this:
<title><?php wp_title(); ?></title> as per http://yoast.com/wordpress-seo-plugin-theme-integration-guide/