Go to
Federal Taxes->Deductions & Credits->Medical->HSA, MSA Contributions and restart the HSA interview.
You will need to click "Edit" on the first screen in order to restart the interview.
Proceed until you come to a screen entitled "
Did your employer tell you about any other contributions?"
Click on "yes".
This will reveal three more lines of data entry below. The third line ("Employer and payroll contributions not reported in Box 12 of your W-2") is where you enter employer contributions to your HSA (i.e., pre-tax) that were not entered with a code of "W" in box 12 on your W-2.
