Form 8889-T and 8889-S (for taxpayer and spouse) is filled in primarily in the HSA interview. You can find this interview by going to Federal->Deductions & Credits->Medical->HSA MSA Contributions. Be sure that you go all the way through the interview until you are returned to the Deductions & Credits menu ("Your Tax Breaks"), since there are questions all the way to the end that affect your form 8889.
