new to javascript – using in instead of functions.php, not loading correctly

1. Start by putting your JS in an appropriate .js file in your theme directory.
2. Use the wp_enqueue_scripts hook (this is where you will enqueue/load any of your custom javascripts).
3. Within that hook, use wp_enqueue_script() to load your script(s).

Example:

add_action( 'wp_enqueue_scripts', 'enqueue_my_stuff' );
function enqueue_my_stuff () {
    wp_enqueue_script('slug_for_your_script' , get_template_directory_uri() . '/path/to/yourscripts.js', array('jquery') );
}