Box 12 code W of your W-2 includes both your employer and employee contributions -- they are all considered to come from your employer (including via voluntary salary reduction with the employer making the contribution for you.) Same for form 5498-SA == your employee contributions were already subtracted from your taxable pay in box 1, and accounted for in box 12. You can't deduct them twice.
Later in the program you only enter additional out of pocket (after tax) contributions.
Entering your contributions twice results in a letter from the IRS assessing tax, interest and a penalty.
