Refund rejected, but I paid the $ due at the time when I submitted. Attempted to refile, but it is asking for the whole payment, even though partially paid. What to do?

How did you pay?   If you "paid" by entering banking information for a direct debit, the payment was not made from a rejected tax return.  When a tax return is rejected nothing at all is transmitted to the IRS.  Please explain what you did to pay your tax due.

Thanks for the response. The amounts were taken from my bank account. I checked to see if they had been debited from the account back in April, and both the state and Federal were taken. I also checked to see if they were returned, and neither were returned. Thanks again for the response.