If your 1099-R is coded as a normal distribution, in the follow-up questions after entering the info from the form, is where you specify what you did with the funds.
Indicate that the amount of RMD is the same amount you rolled over to QCD, and that the balance was rolled over to another IRA.
Go through the screens carefully, and pay close attention to the questions.
Here's some info on Traditional IRA to Roth IRA Conversions and RMD is not listed on my 1099-R.
You should end up with the correct amount showing as taxable on Form 1040.
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