The amount with code "W" in box 12 in your W-2 is the sum of the contributions your employer made and that you made through a payroll deduction scheme.
However, the IRS, by default, assumes that these contributions are taxable until you complete the form 8889.
In TurboTax Deluxe, you enter the data to complete form 8889 by going to Federal Taxes->Deductions & Credits->Medical->HSA, MSA Contributions and entering the interview
Be sure that you complete the interview. This is because the IRS, by default, also assumes that if you don't enter the amount of your qualified medical expenses (which is one of the last questions in the interview), that the amount you had distributed is all taxable.
