Roth IRA Excess Contribution 2018

My husband and I are 62, and both have Roth IRA's.  In 2018, we made our usual contributions.  We  actually made more money than usual and should not have contributed.  But when we did the taxes in TurboTax, we somehow skipped the sections on IRA Contributions and did not enter our Roth IRA Contributions.  We filed our taxes in April of 2019, and did not realize the error until July of  that year. 

 

In July of 2019, we withdrew the contributions and the earnings from both our IRA's and put it into a brokerage account.  We have now received 1099R's,  with a distribution code of PJ, with the amount that we withdrew.

My question is how do we correct this going forward.  Do we refile 2018, entering in our Roth Contributions?  Will TurboTax let us indicate that the money has been withdrawn, and will we have to pay a penalty for those contributions?    And on our 2019 taxes, do we need to add the distribution earnings as income? 

Thank You!