It would have to be entered either as a payment with an extension or as estimated payments. I don't think payments for the tax due would fit under those categories. How did you make the extra payments? What reason did you pick on the IRS Direct Pay? It needed to be a Balance Due payment. So I think on your tax return you don't enter them and say you will mail a check for the whole amount and the payments should match up at the IRS. Then mentally subtract what you paid from the tax due on 1040 line 37 to see if you owe any more.
