IRS sent me a notice that I have to pay due tax with penalties and interests. I paid it online to IRS but like to amend my return. How to amend the amount already paid?

[Vanessa A]

As you walk through the steps in the amend process, you will get to a question that asks how much you already paid with extension or after you filed your return.  This will end up going on line 16 of your 1040X.  

[taxman2011]

It appears in 1040-x line 12:
Payments
12 Federal income tax withheld and excess social security and tier 1 RRTA tax withheld. (If changing, see instructions.) 

and then
16 Total amount paid with request for extension of time to file, tax paid with original return, and additional
tax paid after return was filed . . . . become Zero.

[Vanessa A]

Did the IRS ask you to amend or are you doing so because you disagree with their statement?

If they did not ask you to amend and you do not disagree with their statement, then you would just need to contact them and verify that they received any additional payments.  This may be a timing issue?

[taxman2011]

Thank you Vanessa!

IRS did not ask for amend. I filed my 2020 with COVID-19 claims since I did not received them during lockdown. IRS not only canceled my COVID-19 claims, but also asked for tax due with penalty and interests. I paid IRS in full in order not to pay more penalty and interests but I am amending because I disagree with their statement.

[Vanessa A]

Are you amending back to what it originally was?  If so, that probably won't work since they already disagreed with you.  There should be a statement on the letter that says if you disagree with us take these steps.  Those are the steps you need to take.

[fanfare]

If you are amending, subtract the penalty Line 38 from amount you paid.

Do not try to calculate a new penalty; IRS wlll do that and send you a bill or refund.