No, you don't amend the return at this point, that might makes thing a bit messier.
The IRS has your payment on record and will adjust for it.
They will send the reduced refund (or a tax bill) with a letter explaining the change.
You will have the opportunity to accept the change, or appeal.
The return may take longer to be processed. All you can do is wait.
IF YOU WILL NOW OWE, make sure you get that tax payment paid before April 18th. The payment can be sent in without an amended return.
Ways to pay the IRS