After searching i found this tutorial http://magento.ikantam.com/qa/how-add-discount-total-magento.And on Discount model class i can add/subtract custom price to cart total like :
public function collect(Mage_Sales_Model_Quote_Address $address) {
if ($address->getData('address_type') == 'billing')
return $this;
$discount = Mage::helper('my_module')->getCurrentdiscount(); // Custom percentage
$grandTotal = $address->getGrandTotal();
$baseGrandTotal = $address->getBaseGrandTotal();
$totals = array_sum($address->getAllTotalAmounts());
$baseTotals = array_sum($address->getAllBaseTotalAmounts());
$address->setFeeAmount(-$totals * $discount / 100);
$address->setBaseFeeAmount(-$baseTotals * $discount / 100);
$address->setGrandTotal($grandTotal + $address->getFeeAmount());
$address->setBaseGrandTotal($baseGrandTotal + $address->getBaseFeeAmount());
return $this;
}