Enter the 1099-R, exactly as received. A follow up question, in the interview, will allow you to enter the amount of the Qualified Charitable Distribution (QCD). TurboTax (TT) will put the total amount, of the distribution, on line 4a of form 1040, with the net taxable amount on line 4b, with the notation QCD on the dotted line.
You will not see an actual "deduction" anywhere on the tax form. For most people, the difference between line 4a and 4b is your "deduction". However if your IRA had a cost basis (non deductible contributions made in the past), part of the difference will be the tax free part of the distribution due to the basis calculation.
