need help to fix php issue.

Hello all, I face problem with wordpress navigation bar. When I create new page, it automatically add on navigation bar. but I can't remove one. I saw nav menu don't getting form Appearance menu. Here I add code from header. please give me suggestion where is my wrong, how could I write correct code to get nav menu form appearance menu.

    <nav id="site-navigation" class="main-navigation" role="navigation">
    <ul id="menu-breakthrough" class="nav-menu"><?php
        $mypages = get_pages('parent=0&sort_order=DESC&sort_column=menu_order&exclude=58');
            foreach($mypages as $page)
            {
                echo '<li id="menu-item-'.$page->ID.'" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-'.$page->ID.'"><a href="http://'.$_SERVER['HTTP_HOST'].'/'.$page->post_name.'/">'.$page->post_title.'</a>';
                 $querystr = "
                SELECT option_value
                FROM  `wp_options`
                WHERE  `option_name` =  'ep_exclude_pages'
                LIMIT 0 , 30
                 ";            

                $wp_options = $wpdb->get_results($querystr, OBJECT);          
                $children = get_children(array(
                                'post_parent' => $page->ID,
                                'order' => 'ASC', 'orderby' => 'menu_order ID',
                                'post_type'   => 'page',
                                'numberposts' => -1,
                                'post_status' => 'any',
                                'exclude'      => $wp_options[0]->option_value
                            ));      

                if( count( $children ) != 0 ) {
                    echo '<ul>';
                                //echo '<li id="menu-item-'.$page->ID.'" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-'.$page->ID.'"><a href="http://'.$_SERVER['HTTP_HOST'].'/'.$page->post_name.'/">Who We See</a>';
                    foreach($children as $page2)
                    {
 echo '<li id="menu-item-'.$page2->ID.'" class="menu-item menu-item-type-post_type menu-item-object-page menu-item-'.$page2->ID.'"><a href="http://'.$_SERVER['HTTP_HOST'].'/'.$page->post_name.'/'.$page2->post_name.'/">'.$page2->post_title.'</a>';  }
                    echo '</ul>';
                }
                echo '</li>';
            }
        ?>
    </ul>
    </nav>

PHP:

 

SHould have read your message first. ignore my last comment.