The code W amount in box 12 of your W-2 is the amount of "employer" contribution, that is, the amount that your employer contributed to your HSA PLUS the amount you contributed through payroll deduction (it's the IRS' terminology).
I bring this up because the code W amount is removed from Wages in boxes 1, 3, and 5 on your W-2 before your W-2 is even printed.
This is why there is no "deduction" per se for the code W amount, because the code W amount was never in your income in the first place.
To answer one question - you can't tell from looking at the W-2 if your employer made the W-2 out correctly, that is, did your employer removed the code W amount from Wages in boxes 1, 3, and 5. You have to ask your employer.
Having said that, there is a line for HSA deduction on line 13 on Schedule 1 (1040), but only HSA contributions you made directly to the HSA custodian will appear there.
When you do your tax return, TurboTax may likely find that you made excess contributions, if the code W amount was not changed. TurboTax will automatically add the excess back to income (remember, it was taken out of income on your W-2, so the excess has to be added back). However, it is also likely that the amount you had the employer withdraw was not the same amount that TurboTax thinks was in excess. This can causes issues, like you being unable to tell TurboTax that you withdrew an excess larger than what it determined the excess to be. TurboTax won't accept your entry in this case.
Well, when you get to that point, you may have to come back and talk about it.
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