I personally made contributions to my HSA, thru payroll deductions. I have a 5498-SA of these. where do I account for them?

Look at box 12 of your W-2 for an amount with code W. Those contributions should be reflected there. 

Contributions made through your employer by payroll deduction are deemed to be employer contributions that your employer excludes from box 1 of your W-2.  These are not to be entered as personal contributions in TurboTax.

do not duplicate the 5498-SA, it reports the same HSA contributions made through your payroll deductions and any employer match. However, if you made personal contributions not through the employer they would go on line 2 of the 8889