If you're using TurboTax and apply your 2020 refund to tax year 2021, it's not messy at all. TurboTax stores the information and when you do your 2021 income taxes, the 2020 refund will be applied to your 2021 return.
However, if you don't think the PA 2020 refund will be sufficient to cover your PA estimated taxes, by all means, also pay estimated taxes.
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