It's very straightforward. An RMD is not a special withdrawal or special procedure. It is simply the minimum amount you must withdraw under the regulations. You can always withdraw more.
Suppose the owner has an RMD of $5000. That would be satisfied if they made a withdrawal of $5000 on December 29. But it would also be satisfied if they withdrew $30,000 in March to buy a car, or if they withdrew $500/month over the year for regular living expenses.
Suppose the owner's RMD in your case was $5,000 and the total balance was $50,000. You should consider that you withdrew the $5,000 RMD, plus an additional $45,000. No problem.
This is only important because there are things you can't do with the RMD portion (like contribute it to a new IRA in your name). But you can do those things with the other portion. So if Turbotax knows that $5000 was the RMD portion and $45,000 was just a withdrawal, it will check to make sure that any other transactions are covered by your other earnings or the other withdrawal, and not the RMD.
