We are not given the opportunity to deduct the QCD amount when the 1099-R is imported. After importing the 1099-R amount, you need to click on the "Wages & Income" sub-tab (upper left on the page) then click "Update" on the "!RA, 401K, Pension Plan Withdrawals (1099-R) line in the "Retirement Plans and Social Security" Section.
Doing the update can be confusing but stick with it. Replace the amount in box 2a with the taxable amount (Gross Distribution minus the total QCD). No other changes on that page is typically needed to adjust for the QCD. When you click "Continue," Turbo Tax will eventually ask if a charitable contribution was made.
What's confusing is that, when you go back to the "Wages & Income" list, all distributions (QCDs, return of excess contribution, etc.) are shown even though a portion of that amount is not taxable.
