Amended amount of tax due

I received a letter from the IRS that I missed a form when doing my 2017 taxes. I paid what they said I owed immediately to stop the interest accruing and then obtained the form and did an "amended return" in the Turbotax system to see if I got the same numbers. Now I just need clarification for this example: Say IRS says you owe $6,000 based on this omission and you do the Turbotax check and it says you owe $4000 is that because I had gotten a refund of $2,000. In other words, does Turbotax show only the difference, not what the overall tax bill would have been?