That was dumb of them since only 1 1099-R was required. On the first 1099-R, you indicate that the box 1 amount was an RMD and that the entire gross amount applies to the RMD. Do the same with the QCD, but indicate the amount of the QCD. The totals of box 1 for both should equal the RMD for the year.
The other workaround would be to combine the amounts in each box on the two so there would be only 1-1099-R in Turbotax.