How do i properly make sure that my hsa contributions are being counted as a deduction in my 2018 taxes?

There are two ways to make HSA contributions: through your employer and directly to your HSA.

If you make contributions to your HSA through your employer (whether it is your employer's contribution or yours through payroll deduction), this appears as an amount with the code of "W" in box 12 on your W-2.

When your employer prints your W-2, he/she removes the code W amount from Wages in boxes 1, 3, and 5 on your W-2. This is why you don't see a deduction on your tax return for these contributions - because they were never in your income in the first place.

If, on the other hand, you made contributions to your HSA directly to the HSA custodian (not through your employer), then these contributions appear on line 12 on Schedule 1 as an adjustment (reduction) to adjusted gross income (AGI). You enter these contributions on the screen with the heading "Let's enter [name]'s HSA contributions" on the second line where it says "personally" (see screenshot below).

[Edited 4/1/2020 2:27 pm CDT - updated for 2019]