If you have already filed the 1040X with an incorrect amount paid on line 16 then there is nothing you can do at this time but WAIT for the IRS to process the original return to note the payment that was not made and then to process the amended return ... they should correct the line 16 amount automatically. Do NOT send yet another amended return as this will only make things worse.
In the meantime print off a copy of the 1040X and manually correct the line 16 amount then complete the rest of the form to see if you really do have a refund on the amended return or just owe less. Simply follow the line instructions on the form ... they are simple math entries.
