Instead of adding your theme javascript manually in the header.php/footer.php, a better way is to enqueue the files, so that they are loaded via wp_head() or wp_footer().
Here is how – add the following to your theme’s functions.php:
/* Enqueue javascript
/* ------------------------------------ */
function alx_scripts()
{
wp_enqueue_script( 'flexslider', get_template_directory_uri() . '/js/jquery.flexslider.min.js', array( 'jquery' ),'', false );
wp_enqueue_script( 'scripts', get_template_directory_uri() . '/js/scripts.js', array( 'jquery' ),'', true );
if ( is_singular() && get_option( 'thread_comments' ) ) { wp_enqueue_script( 'comment-reply' ); }
}
add_action( 'wp_enqueue_scripts', 'alx_scripts' );
In this example I am loading flexslider in the header, and a general theme scripts file in footer. So, if you set to true, it will load in the footer.