Go to
Federal Taxes->
Deductions & Credits->
Medical and enter the "HSA MSA contribution" interview screens. One of the first things that you are asked for after saying that you have an HSA is the information from your 1099-SA.
The information in this section will populate form 8889, which is how contributions to and distributions from your HSA are reported.
Please be sure to go all the way to the end of the interview before exiting.
