I think I'm clear on it now...
For only 1099-Rs that show an RMD deficit, when TTax asks for the RMD for that one account on the "Let's get more information..." page, you need to put in a value that is greater than zero, but less than or equal to the distribution from the account (even if the actual value of the RMD should be higher). Entering the amount of the entire distribution satisfies this.
TTax will then cancel out any tax that it had previously calculated for that account, remove the Form 5329 from your return, and you will see your Federal tax bill adjusted accordingly. Certainly on my fairly simple return there are no mentions of RMDs anywhere else so this information is not passed on to the IRS. However RMD data is sent to the IRS by investment companies. So if you are in RMD deficit over your entire IRAs it's probably not a good idea to do this.
Thanks to all who have responded.
