Your payroll contributions will be recorded in box 12 of your W-2 with a code W and Turbotax will automatically pick them up. In Turbotax, your medical expenses are reported on the Deductions and Credits page in a section for HSA/MSA contributions. You will first be asked if you had withdrawals from an HSA, which will be reported to you on a form 1099-SA sent by the plan administrator. After entering the withdrawals, there is a box to check for "Yes, I used all the withdrawals for medical expenses." (Don't skip this or the money will be taxed.) Keep going and it will next ask if you made any out of pocket contributions. All this information will go onto a form 8889 as part of your final tax return.
