I'm not sure exactly what you are asking. Any HSA contributions shown in box 12 of your W-2 with code W are called "employer contributions," even if part or all of it came out of your pay. The amount from the W-2 should be on Form 8889 line 9. If you made contributions directly to your HSA, not through payroll, that would be on Form 8889 line 2.
Are you trying to fill out Form 8889 in forms mode? That's likely to lead to errors. I suggest that you enter your HSA information using the Step-by-Step interview instead.
The TurboTax Accurate Calculations Guarantee will not apply if you make a mistake entering information in forms mode.
