Roth IRA excess contributions - How to pay excise penalty for multiple years?

We made ineligible contributions to a Roth IRA in three separate years (2017, 2018, 2019). We removed those contributions and associated earnings in a single transaction in January 2021. How and when do we pay the excise penalty using Form 5329?

Will we:

• Do this just once for our 2021 return, since the distribution income came back to us in 2021?
• Or do we need to amend returns for all three years, using a separate 5329 for each?

Thanks in advance.