It is possible to make contributions to an HSA with "after tax" dollars, by sending the money directly to the HSA custodian to be placed in your HSA account. This amount is reported on line 13 of Schedule 1 (1040). This is what people call a "deduction".
The amount of HSA contributions made by payroll deductions appear on your W-2 in box 12 with a code of W. The code W amount is removed from Wages in boxes 1, 3 and 5 when your W-2 is printed - hence, these contributions might be better called an "exclusion".
Elaine, I am not sure how you made these contributions, but it sounds like you made them directly to the HSA custodian (please correct me if I misunderstood). When your excess contribution is detected by TurboTax in the HSA interview, then the amount on line 13 on Schedule 1 (1040) will be reduced by the amount of the excess.
YOU DO NOT have to do anything about the 8889; TurboTax will handle this automatically (TurboTax will handle the excess automatically if you made the contributions through your employer as well).
You are correct that the HSA is "persistent". This is like an IRA - it belongs to the individual and lasts until you close it.
And please don't be sad that you don't understand all the rules about HSAs - many tax professionals don't either.
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