WooCommerce orders are posts and behave the same as any WordPress post. So you can use the same WordPress functions to update or read the post meta data.
<?php $meta_values = get_post_meta($post_id, $key, $single); ?>
For your example I’d suggest:
$match_order_meta = get_post_meta( $order->ID, 'My_Checkbox', TRUE);
The ‘TRUE’ flag tells WordPress to return the value as a string. Without the TRUE flag you’ll get an array. Again take a look at the docs below.
You might also:
echo '<!-- $order->ID -->';
To make sure you have the correct ID.
Here are the docs get_post_meta().