The value of line 2 is normally the amount of "personal" contributions that you made to the HSA. That is, these are contributions that you made directly to the HSA, NOT through your employer.
You don't enter anything from the 5498-SA; that is an informational form that is sent to you by the HSA administrator that we don't ask for - because the deadline to receive it can be as late as late May (although some HSA custodians send it out earlier).
But, yes, box 2 on the 5498-SA is the total contributions, which should be the sum of your personal contributions and contributions made through and by your employer. But, no, that is not how we determine the value of line 2 on the 8889 - this line comes from the second line on the screen headed "Let's enter your HSA contributions" (see screenshot below). The first line on this screen comes from the W-2 in box 12 with a code of W and the second line on the screen comes from you (i.e., you enter your direct contributions here).
This second number flows directly to line 2 of the 8889.
