add_action('wp_head', 'amazon_checkout_position');
function amazon_checkout_position() {
    ?>
    <script type="text/javascript">
        (function($) {
            $( document ).ready(function() {
                $('.wc-amazon-checkout-message').appendTo('form.woocommerce-checkout div#order_info_col2');
            });
            $('.wc-amazon-checkout-message').contents().filter(function () {
                return this.nodeType === 3;
            }).remove();​​​​​​​
        })( jQuery );
    </script>
    <?php
}