You do have an HSA. You can't say that you don't. The contributions are shown in box 12 of your W-2 with code W. Those contributions are already excluded from the amount of wages shown in box 1 of your W-2, so they will not be taxed. The only thing you have to do to prevent your contributions from being taxed is to enter your W-2 accurately.
When you correctly say that you do have an HSA, you will be able to enter your 1099-SA and specify the amount that you spent for qualified medical expenses.
