jQuery(document).ready(function($) {
    // your code
});

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()`
);

wp_enqueue_script( 'yourscripthandle' );