If your checks have not already cleared your bank account, you could place a stop-payment on them. If both, payments made through direct debit and check, have already been debited from your account you'll likely receive a letter from the taxing authorities asking how you'd like them to handle the overpayments. I'd advise you call the IRS (1-800-829-1040) and your state taxing authority now and request refunds of the overpayments.