All 1099-R's look basically the same, and are entered in the same place in TurboTax.
If there is a different amount in Box 2a (taxable amount) than Box 1(distribution), that's an indication that there is a basis in the account (after-tax contributions). If that applies, TurboTax asks questions to verify that the amount in Box 2a is the correct taxable amount (it usually is).
Sometimes the 1099-R has 'taxable amount not determined' checked and Box 2a is blank. In that case, TurboTax will ask follow-up questions to determine the taxable amount. Normally, it's the amount in Box 1.
Also, the Code in Box 7 distinguishes different types of distributions.
Enter the 1099-R exactly as shown (be sure to check the IRA box, if it's checked on your document).
Pay close attention to the follow-up questions TurboTax asks after entering your 1099-R.
You don't need to track the after-tax amount; the Plan Administrator distributes a % of after-tax contributions each year, based on the rules for that type of account.
Here's more detailed info on Form 1099-R.
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