Simply indicate that the distribution from the larger IRA was some or all RMD and indicate that either the entire amount was RMD or, if the distribution was more than your combined RMD, indicate the amount that was your combined RMD. After clicking the Continue button on the Your 1099-R Entries page, indicate that you satisfied all of your RMD with respect to your IRAs.
There is no requirement to report the specific RMD amount that applies to each IRA, only the total.