The 5498-SA documents total contributions to your HSA as well as the value of the HSA on December 31, 2016.
Most taxpayers have the contributions documented with a code "W" in box 12 on their W-2. And if the taxpayer made any contributions outside their employer, they should know what it is from their checking account statement.
So you don't enter the contributions from the 5498-SA. Indeed, the IRS does not require the 5498-SA to be sent to you until May 31st, because you can make contributions to the 2016 HSA until April 18, 2017.
As for the HSA value at the end of the year, the only taxpayers who need that are those who have an excess contribution which they can't withdraw - a fairly small percentage.
So the 5498-SA is mostly for your own records.
The 1099-SA, as you probably know, reports on distributions from your HSA. You do have to enter this form.
