I was told to input the 1099R the way it is with the $400 in box 5. My IRA administrator put the $400 in the Roth IRA already, so it is separated from the rollover IRA. The form 5498 from the IRA administrator shows the total rollover amount minus the $400 that went into the Roth IRA on box 2 "rollover contributions". So I think I am ok. I am not familiar how TurboTax tracks and compute the input data. You may want to re-post your question so it would be more visible to the employee tax experts and others to answer your questions.
