The best practice is the following:
Put your Javascript code in a file, yourcustomjs.js, and store it in your theme folder. I would recommend yourtheme/js/yourcustomjs.js.
Be sure that you wrap your script, where needed, in a Document.ready function like the following:
jQuery(document).ready(function($) {
// your code
});
This enables you to ensure the $ shortcut is working.
Afterwards you need to register and enqueue your script. Usually, you do this in your functions.php, but I always recommend to create a file yourtheme/library/scripts.php, which is included in functions.php. This allows you to handle all the Javascript files in one place, with no additional stuff around it.
In your scripts.php you have to register your Javascript within WordPress.
wp_register_script (
'yourscripthandle', //string $handle: a string to identify this script
get_bloginfo( 'template_url' ) . '/js/yourcustomjs.js', //string $src: Path of your script file
array ('jquery' ), // array $deps = array(): defining which scripts your script is dependend on. In your case, it's jQuery.
'', // string|bool $ver = false: The version of your Script
true //bool $in_footer = false: whether your script should be enqueued in `wp_head()` or `wp_footer()`
);
Now WordPress knows about your script, and you need to tell WordPress to output it, and this is done with wp_enqueue_script():
wp_enqueue_script( 'yourscripthandle' );
There you go! If you followed the steps correctly, your script should be loaded in the footer.
BTW: analogous to registering and enqueueing scripts, you should do the same with wp_register_style() and wp_enqueue_style()