Estimated payments were all due by Jan 15 and this is April. You do not want to enter your tax due on the return as an estimated payment. When you go to the IRS website, it will ask what you are paying. You want to pay your tax bill for 2021.
When you tell the program that you are going to pay by check, you are just telling the program. It has nothing to do with your tax return and what the IRS receives. Otherwise, select to pay by debit and enter your bank information so the IRS can draft your account. The IRS receives either instructions to debit your account or no instructions from the section. The IRS knows you can pay in person many places, credit, draft, payment plan, etc. See Payments.
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