Entry: https://proconnect.intuit.com/community/form-1099-r/help/how-to-enter-coronavirus-related-retirement...

The withholding is a tax payment; it doesn't relate to taxes owed. You just fill in the tax form for how you want treatment. Then, any payments made on their behalf through any combination of withholding and estimates, will be used as always = against taxes owed or overpaid.