How do I input the employee contributions from my HSA?

Your W-2 should already include the HSA contributions from both you and your employer.  Adding it again will double-count it. 

The only time you will add additional personal contributions is if you made a separate contribution directly to the HSA, bypassing withholding. ‌If you did this, go to Deductions & Credits, then HSA, MSA Contributions and report the amount in the interview screen "Let's enter your HSA contributions" in the box for "Any contributions you personally made (not through your employer)."

Check that the contributions in Box 12 Code W agree to your records.