i am using this code
$order->setTotalPaid($totamount)->setBaseTotalPaid($totamount); $order->setState('pending_validation','pending_validation', true); $order->save();
to pay the order amount. and also setting order status to Pending Validateion (custom order status).
After this i gose to magento backend and setting its payment validated. and order states gose to processing. then i try to create invoice, its order amount is doubling.