If you are in the HSA interview on the screen entitled something like "Let's enter [name]'s HSA contributions", you would enter here ONLY HSA contributions that you made that are not on your W-2 (i.e. contributions that you made directly to the HSA, not through your employer).
Your 2016 employer and payroll contributions are on your W-2 in box 12 with a code of "W". The dollar amount that is with the code W should appear on the screen described above in the first line "2016 employer and payroll contributions". You do not have to enter that amount again.
The confusion is caused by the fact that your employer contributions to your HSA and your contributions to the HSA through a payroll deduction scheme are both described as "employer" contributions.