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After you file
TT calculates an estimated underpayment penalty based on your entries in the program however the feds & state reserve the right to access a final underpayment penalty, late filing penalty or late paying penalty ( plus interest ) based on the info they have and when the balance due was actually paid. https://www.irs.gov/individuals/understanding-your-cp14-notice
For instance, if the 2017 program said you should pay $1000 a quarter and you transferred in that info to the 2018 program then the program calculates the penalty on the $1000 a quarter you were supposed to pay ... however if you did not pay those payments timely and did not correct the program's assumption that you did (maybe you missed the april payment but caught up on the june payment ... or paid it all on one payment in January) then the fed/state know this and made the correction and billed you accordingly.
To see whether a payment has posted or view your overall balance, you can use the Get Transcript tool to request a Tax Account Transcript or Record of Account Transcript.