I have two SEP-IRAs with RMN requirements, a large one at a large investment firm, and a smaller one held as CDs at a small local bank. I paid the the RMN for both accounts from the large SEP-IRA, with most of the money going to charity and some being cashed out and transferred to a non-retirement investment account. There is no way to report this on TurboTax Desktop. It only allows me to report payments from the larger SEP-IRA. I was able to file this for my 2023 taxes, but TurboTax now asks more details that I can't answer.
You can withdraw your RMD 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.