The total of what your employer contributed to your HSA plus whatever you contributed through payroll deduction is supposed to be in box 12 on your W-2 with a code of W. You should not enter this code W amount anywhere else on your return.
The amount that you (all) contributed through payroll deduction is called "the employer contribution", even though you made some or all of it. In this case, "the employer contribution" means that this number will be removed from Wages in boxes 1, 3, and 5, so they are not taxed. This is IRS terminology, which is the source of infinite confusion.
In any case, if the code W amount includes your payroll deduction, then everything is OK. There is NO need to enter your contributions anywhere else.
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