Yes, the IRS would have applied your 2020 payment to your 2021 tax balance if you designated it that way.
This payment should be reported on Form 1040 Line 26 (2021 estimated tax payment and amount applied from 2020 return) rather than on Schedule 3 as an Other Credit.
Go to Deductions & Credits >> Other Income Taxes >> 2020 refund applied to 2021 federal taxes, and enter the amount you paid. Although the description doesn't exactly match your circumstances, your entry will report your payment on the correct line of your 2021 return.
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