If you want to run SQL queries in Magento, you don't need to know the value of your table_prefix located in the app/etc /local.xml. Magento allows you to read the full name (including table_prefix) of your tables.

<?php

$coreResource = Mage::getSingleton('core/resource') ; 

echo $coreResource ->getTableName('sales_flat_quote_payment')  WILL return mgn_sales_flat_quote_payment where "mgn_" is the table_prefix. 

// fetch write database connection that is used in Mage_Core module
$write = $coreResource->getConnection('core_write');

// now $write is an instance of Zend_Db_Adapter_Abstract
$query = "UPDATE  `".$coreResource->getTableName('sales_flat_quote_payment')."` ........ ";
$write->query($query);
?>