Meta title and description not working

I am using Yoast SEO and a custom header.

this obv means that any code that yoast uses to input all the seo stuff such as title tag and meta description wont be there.

I solved the title tag by using this code:

<title><?php
    /*
     * Print the <title> tag based on what is being viewed.
     */
    global $page, $paged;

    wp_title( '|', true, 'right' );

    // Add the blog name.
    bloginfo( 'name' );

    // Add the blog description for the home/front page.
    $site_description = get_bloginfo( 'description', 'display' );
    if ( $site_description && ( is_home() || is_front_page() ) )
        echo " | $site_description";

    // Add a page number if necessary:
    if ( $paged >= 2 || $page >= 2 )
        echo ' | ' . sprintf( __( 'Page %s', 'twentyeleven' ), max( $paged, $page ) );

    ?></title>

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and that seems to work.