How to Javascript/jQuery

Just paste this in your functions.php file. It will automatically add jQuery in your theme.

function wcs_scripts_styles() {
    wp_enqueue_script( 'jquery' );
}
add_action( 'wp_enqueue_scripts', 'wcs_scripts_styles' );

WordPress automatically include jquery from it’s location. You do not need to upload jquery on your theme.
additionally you can also add more scripts lile this.

function wcs_scripts_styles() {
    wp_enqueue_script( 'jquery' );
    wp_enqueue_script( 'new-script', get_template_directory_uri().'/js/new-script.js', 'jquery', NULL, true );
}
add_action( 'wp_enqueue_scripts', 'wcs_scripts_styles' );

In this code new-script.js is in theme\your-theme\js\ folder. You can similarly add more js files like that.