A check from your checking account to your HSA is an "after-tax" contribution. As such,
it is reported on the second line of the screen entitled "Let's Enter [name] HSA contributions" (see screenshot below) - "Any contributions you personally made (not through your employer)".
This amount will appear on line 25 on your 1040 where it will reduce adjusted gross income.
The 1099-SA reports on distributions, not contributions.
The question you are referring to is in the section where TurboTax asks more questions about your HSA (i.e., it's finished with the 1099-SA).
The amount on the first line ("2016 employer and payroll contributions") will be the amount in box 12 on the W-2 with a code of "W".
