I would suggest you file amended returns for each year and pay in the penalty year by year. At the top of part IV of form 5329 you are instructed for report information for the current year and carryover information from the previous year. The penalty for 2019 is all that should be reported on the 2019 tax return.
You can prepare amended returns in the online TurboTax for free as follows:
1. Log into your TurboTax program
2. Find "Your Tax Return & Documents" on your home page
3. Click on the "Show" option
4. Select the year you want to amend
5. You will see an option to "Amend(change)" the return for that year.
6. Just follow the instructions to start the amend process.
In the desktop version of TurboTax, look in "Other Tax Situations" for the amend return option
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