I had a similar problem. All I had to do to clear myself with the IRS was send them a copy of the Explanation Statement listing each of the QCD charities I contributed to and the amounts given to each. That form will pop up on TurboTax if you click "Explain" next to QCD on Form 1040. The Explanation Statement has no form number but is listed in the list of forms on TurboTax at the very bottom. Also, when you e-file and choose all forms that are required, the Explanation Statement will be sent (or should be) to the IRS.
The IRS could obviate the necessity of sending this form if it changed the 1099-R to include a check box showing that a part of the RMD is QCD payments and then the total amount of those payments. That way the IRA custodian will be giving the IRS all the info it needs when it sends a copy of the 1099-R to the IRS.
