/**
 * Add the field to order emails
 **/
add_filter('woocommerce_email_order_meta_keys', 'my_woocommerce_email_order_meta_keys');

function my_woocommerce_email_order_meta_keys( $keys ) {
    $keys['Gift wrap?'] = 'my_gift_wrap_checkbox';
    $keys['Gift wrap instructions'] = 'my_gift_wrap_field';
    return $keys;
}