Solved
can i mentioned somewhere in the form that i am making a online payment(both federal and state). is the online payment applicable to both federal and state(i am from MA)
No, it will not be an issue. You can add a note that the payment was made online and when they process the return they will net all payments received for 2016 to complete the process. At that point it should result in zero balance due with your online payment accounted for. I assume the state would process the same way.
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