You need to add a new collector after the total total (Mage_Sales_Model_Quote_Address_Total_Grand). He must change the amount set by the great collector.
MageConf . , -, . , .
, . (. config.xml module etc) <before>subtotal</before> node, <after>grand_total</after>) () , :
$address->setGrandTotal($someValue);
$address->setBaseGrandTotal($someBaseValue);
, , . , . ( fetch()) , .
:)