After you enter the Form 1099-R for the distribution, continue through the questions in the interview. When it asks "What Did You Do With The Money" select "I moved the money to another retirement account," even though you didn't move all of it to the Roth IRA. It will then give you three choices. Select the third choice, "I did a combination of rolling over, converting, or cashing out the money." It will then ask you how much you rolled over or converted, with separate boxes to enter a rollover amount and a Roth conversion amount. Enter the amount that you converted to the Roth IRA in the appropriate box, then click Continue.
The next screen will ask whether your put the money into an HSA. Again, select "Yes, I put this money in an HSA," even though you didn't put it all in the HSA. It will then ask you how much you put in the HSA. Enter the amount and click Continue.
Be sure to continue going through all the questions, even after the summary screen that lists your 1099-R entries, until you get to the income summary screen.
