"However, nothing changed on the taxes owed when I entered the QCDs,"
Exactly what do you mean by that? When you enter a From 1099-R that is all QCD, your tax liability shouldn't change because the QCD amount is not included in taxable income. If the amount entered was not being treated as a QCD, your taxable income would increase and, generally, so would your tax liability.
As long as the QCD notation is present next to Form 1040 line 4b and line 4b excludes the amount of the QCD, everything is being handled correctly. You do not also get to treat the QCD as a charitable contribution on Schedule A.
