" In order to pay the 6% penalty, for 2019, wouldn’t my penalty be 0? Because the account balance year end statement of 2019, shows IRA balance = 0 as I deposited for the first time in 2020, towards 2019."
No. For the purpose of determining the penalty for 2019, the contribution made in 2020 for 2019 is required to be added to your 2019 year-end balance.
Assuming that you had no other excess contributions and had not reached age 50 by 2021, your penalty is $360 for each year 2019, 2020 and 2021 for a total of $1,080. You need to file 2019, 2020 and 2021 Forms 5329 to report and pay this penalty for each of these years.
You didn't ask about 2022, so I assume that in 2022 you either received a regular distribution of $6,000 or were about to apply the excess $6,000 as your 2022 Roth IRA contribution, eliminating the excess for 2022 and beyond.
