TT does ask this and it is reflected on different lines on Form 8606. Not sure all the ramifications, but certainly matters in terms of penalties if you are doing Roth IRA conversion before age 59.5 which would not be penalized vs. taking an early distribution (the 1099-R will be coded differently in Box 7 also I think).
After inputting the 1099-R there should be an interview question which starts "what did you do with the money..", you select "I moved the money to another retirement account", then "I did a combination of rolling over, converting or cashing out the money" and then you can specify the amount converted to Roth IRA. This will flow to Line 8 on your Form 8606 etc.
