Multiple IRA's generate separate MRD's and Penalties

Turbo-Tax needs to fix this program problem. I have a traditional IRA, a Rollover IRA and a SEP at two different brokerages. Turbo Tax asks for balances separately and calculates MRD's separately. The program assumes that the required distributions will be made from the corresponding accounts and calculates a penalty when the distribution fall short of that calculated.   The IRS permits drawing distributions from any single or combination of accounts as long as the total obligation is satisfied. There is no obvious provision in the program for satisfying multiple MRD's from other than the associated accounts.