All amounts contributed via payroll deduction, both your money and free money from the employer, are considered employer contributions. Basically, you agree to a salary reduction and the employer contributes the money to the HSA for you instead. You must not enter your payroll contributions again separately. That question only asks about extra contributions you send directly to the HSA bank from your after-tax funds.
If you have been entering your payroll contributions separately, you have been creating multiple errors and you need to go back and amend all those tax returns to correct the errors.