This is a common problem with individuals in the phase-out range. Yes, your amendment must include the penalty on the new excess, calculated on 2017 Form 5329.
You'll owe this same penalty again with your 2018 tax return unless you are able to apply this new excess as a part of your Roth IRA contribution for 2018, reported on 2018 Form 5329. Whatever of this excess has been carried into 2019 will ether have to be applied as part of your 2019 Roth IRA contribution or you'll need to obtain a regular distribution (not a return of contribution before the due date of your 2017 tax return) to resolve the excess for 2019 and avoid another excess contribution penalty for 2019.
If you've already started your 2018 tax return by transferring in your original 2017 tax file, you'll need to tell 2018 TurboTax that you have an excess Roth IRA contribution carried in from 2017 (the amount of the new excess).
