Yes, Form 8606 applies to nondeductible contributions. For Traditional IRAs this is the only real concern for you, so that when you take distribution you are not taxed on this cost in your IRA (amounts you were never able to deduct which became 'after-tax' contributions).
Roth IRA contributions were never able to be deducted, and therefore all of the contributions are 'after-tax'. There is no recordkeeping once you reach retirement age because all distributions, including earnings, is tax free.
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