Your Required Minimum Distribution (RMD) must be calculated separately for each IRA that you own, but the total amount of your RMD can be withdrawn from one of the IRAs.
Your 1099-R should reflect the amount of your Required Minimum Distribution that was required, and that is what you have to report as a distribution.
You should enter your Form 1099-R as it is shown if it reflects the total amount of your Required Minimum Distribution.
Click here for instructions on entering your Form 1099-R.
Click here for information regarding Required Minimum Distributions (RMD's).