Two things:
1. If you go all the way through the HSA interview (do a Search for hsa and click on the jump-to link), you will see a screen with the heading "Let's enter [name]'s HSA contributions".
There are two lines. The first line shows you the amount with code W in box 12 on your W-2. The second line is where you enter the sum of any contributions you made directly to the HSA, outside of your employer.
2. The amounts on your 5498-SA may not reflect your exact contributions. The boxes on the form may have amounts in them other than your personal contributions for the year.
This is why we tell you that you don't have to enter anything from the 5498-SA, because we aren't sure of what we're getting without comparing it to other values.
No, just look in your check book and determine how much you contributed directly to the HSA (not through your employer), and enter on the "Let's enter [name]'s HSA Contributions" (I guaranteed it's there).
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