There is no need to modify the Form 1099-R downloaded from Morgan Stanley. Edit the Form 1099-R, leave the form details as they are, and in the follow-up questions indicate the QCD amount that you had transferred to charity by Morgan Stanley. TurboTax will include the entire box 1 amount on From 1040 line 15a or Form 1040A line 11a but will exclude the QCD amount from the amount on line 15b or 11b. TurboTax will also include the notation "QCD" on the line.
QCDs can only be made from an IRA. The Form 1099-R downloaded from Morgan Stanley will have the IRA/SEP/SIMPLE box marked for any distribution from a traditional IRA.
