After you file

It sounds like you didn't go through the Amendment Process correctly.  Here's info and a video on How to Amend a Tax Return.  Be sure to make a copy of your originally filed return first.

TurboTax does not compare your original/amended returns.  When you Amend, you are add or subtracting info that was not on the original return.  Form 1040X will display in Column B the amount of change to a particular line (in your case, Line 1, Income and Deductions) and Column C shows the corrected amount.  You then add an explanation of what you changed, and why (for example, 'correct 1099-R entry').  

If your 1099-R has Box 2a (Taxable Amount) blank, but Box 2b has 'Taxable Amount is not Determined' do you also have an amount in Box 5?    The Code in Box 7 is important, too.  Be sure to pay close attention to the follow-up questions after your entry. 

Generally, pension income is taxable income, however:

• If no after-tax contributions were made to the pension plan before distribution, the entire amount is generally included in taxable income.
• However, in cases where after-tax contributions were made to an annuity or pension, only a portion of the distribution will usually be taxed.

Here's more info on Pension Income and a detailed article on Form 1099-R.

@ebtz 

Here's more info on