There shouldn't be any problem. The tax return doesn't distinguish between RMD and other withdrawals. It's all just a Distribution. RMD doesn't show up on your tax return. The 1099R will be for one total amount. Turbo Tax will ask you if you took the RMD. Just say yes. It doesn't need to know it's for multiple accounts. If you have withholding taken out you will get credit for it. It will add to your refund or reduce any tax due.
