The surcharge does not appear in emails or templates

Your theme might be from an older version and includes a rewrite of the template. 

You can easily test this by using the default theme and resending the order email and reloading the order view. If the surcharge shows up, please either update your theme to be comparable to the Magento version you are using or add this block:

<?php if ((float) $_order->getFoomanSurchargeAmount()): ?>
    <tr>
        <td colspan="3" align="right" style="padding:3px 9px"><?php echo $_order->getFoomanSurchargeDescription() ?></td>
        <td align="right" style="padding:3px 9px"><?php echo $_order->formatPrice($_order->getFoomanSurchargeAmount()) ?></td>
    </tr>
<?php endif; ?>

The base email templates are here: app/design/frontend/base/default/template/email/order/

Previously all the order totals were added individually similar to the snippet above. In newer versions it has been replaced by:

<?php echo $this->getChildHtml('order_totals') ?>

with additional changes in the layout/?.xml files adding the order_totals