If I meant to file an extension, but instead accidentally submitted my 1040, AND then went back into TurboTax & filed for an extension, what is now the best way forward?

I have already received back notification (from both Fed & State) that my submitted returns were accepted.  Unfortunately, my check (for owed-taxes) was sent along with the extension-application-voucher (to that address, payable to US Treasury)  instead of with the submitted-payment-voucher (to a different address, payable to IRS).  Should I put stop-payment on the 'extension-check' and submit another submitted-payment-check?