Neither the IRS nor TurboTax know what your annual Required RMD is. For each 1099-R you enter, you could say 'Yes, the distribution includes RMD', and 'Yes, the entire distribution is RMD'. Enter the entire distribution amount as RMD amount.
The IRS expects you and/or your plan administrator be responsible for withdrawing your RMD. The IRS states that you can take your RMD from one account, or across several accounts. Here's IRS Requirements for RMD's.
You may need to delete/re-enter your 1099-R's if you're having issues with penalties being generated, and if you're using TurboTax Online, clear your Cache and Cookies.
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