You should receive a 1099-SA from the trustee of the HSA, and you should wait for that. You do need to enter the information off the 1099-SA, and it has nothing to do with whether you take the standard deduction, or not. You have to tell the IRS how the money was used. Work through the "1099-SA, HSA, MSA" interview under the "Deductions and Credits" tab.
Tom Young