Was your donation to the church made by an IRA custodian sending the money directly to the church? If not, the entire amount must be included in income and any deduction for the charitable contribution would have to be taken on Schedule A. If the money was instead properly transferred to the charity by the custodian and qualifies as a Qualified Charitable Distribution from your IRA, the entire amount will be still be reported on single Form 1099-R and in the questions that follow your entry of the Form 1099-R details TurboTax will ask how much you had your IRA custodian transfer to charity. TurboTax will then exclude this portion from your income on Form 1040 line 4b and will include the notation "QCD" next to the line. The remainder will automatically be included on line 4b (assuming no basis in nondeductible traditional IRA contributions).
