Retirement tax questions

This is very helpful.  TT almost made me make an expensive mistake.  I converted 100% of one of my traditional IRAs, which had taxed and pre-tax money.  After answering TT's questions about how much was already taxed, TT asked what the total amount is in all of my IRAs (non-ROTH).  I have another much larger IRA with another company, so I answered with that amount, and in response TT reduced my tax refund by over $1000.  That made no sense to me until I read the answer above.  Now I understand that TT was assuming only a pro-rated fraction of the taxed funds were converted.  However, since at the first company the entire IRA was converted, 100% of the taxed funds were converted.  Thus, the TT question is misleading.