Not entirely sure what you’re asking but you have to include and register scripts and then enqueue what you require like:-

<?php wp_enqueue_script('jquery'); ?>

(Place immediately before <?php wp_head(); ?>).

Which is included with WordPress incidentally.

You can read more on wp_enqueue_script for more information on how to use this in your theme.

Edit

An example of registering javascript in theme’s functions.php

function load_scripts() {
    wp_register_script( 'jquery-slider', get_template_directory_uri() . '/js/jquery.slider.js', array('jquery'), '2.0', true );
}