While entering your form 1099-R, if you have entered a birth date which makes you older than 70 1/2 in the tax year, TurboTax will ask you if any portion of your distribution was transferred to charity. You can then enter the amount transferred to charity. For a QCD, check 1040 line 4b. It should be 0 (unless you have other taxable 1099Rs) and QCD written by it.
To qualify as a QCD, the distribution must have taken place DIRECTLY from the account trustee to the charity. It's ok for them to send you a check made out to the Charity that you then mail to the Charity. Withdrawing funds and then making your own contribution to a charity DOES NOT qualify as a QCD. If you withdraw funds from your IRA and donate those funds to a charity, the withdrawal is fully taxable and you can deduct it as an itemized deduction if you itemize on Schedule A and don't take the Standard Deduction.
