You have two choices:
1. Enter the original medical bills (all of them) in the Medical Expenses interview, then enter the insurance reimbursements at the end when TurboTax asks (the HSA reimbursements from the 1099-SA are subtracted automatically), or
2. Enter the net medical expenses (i.e., net of insurance reimbursements) and a single entry for the bills covered by the HSA in Medical Expenses, with the description of "bills covered by HSA distributions" and the amount in box 1 on the 1099-SA. You would enter the description and the amount at the end of the Medical Expenses interview as a miscellaneous expense.
Since many taxpayers enter only the net medical expenses (not realizing that the subtraction of the HSA distributions is automatic), #2 is easier for most.
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