Form 5329 can be filed stand-alone because it has a signature block, but it you prefer you could file it along with Schedule 2 and Form 1040-X. It won't hurt to do so.
TurboTax automatically prepares Form 8606 Part III and includes it with your tax return when you enter a code-J Form 1099-R. Be sure to click the Continue button on the page that lists the Forms 1099-R that you have entered and enter and confirm you basis in Roth IRA contributions (including the excess contribution).
