You can withdraw from only one account if they are both regular IRAs or 403b plans. If any of them are 401ks or 457 plans or the like then you have to take the required RMD from each account separately.
Make certain that the 'IRA/SEP/Simple' box is checked on all of the 1099Rs that you received and in the TurboTax system. If it is not then the system is doing the correct calculation.
Here is where that information can be found on the IRS website.
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