Again, you do not enter these in the Charitable donations section. Rather, after you enter the 1099-R in Federal > Wages and Income > Retirement, there is a question that addresses this.
In order to be a QCD: (1) the retirement plan administrator must have sent the funds directly to the charities; or (2) sent them to you, but with the checks made payable to applicable charities. If they/you did otherwise, please post back.
