"and zero'd out the 2a box " - are you saying that you wrote over the amount in box 2a because you though it wasn't taxable?
Just leave the 1099-R as is, and in the 1099-R interview - if you are old enough - TurboTax will ask you if you gave this to charity and then you will be able to enter how much was the QCD. Let TurboTax do the work for you.
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