Form 5498-SA does not necessarily have the amount of contributions you personally made. Box 2 contains the TOTAL contributions made by you and your employer through payroll deductions PLUS any contributions you made directly to the HSA in 2018. Box 3 is the total of HSA contributions made to your 2018 HSA in 2019.
There are two major ways to make contributions to an HSA: contributions through your employer and contributions directly to the HSA. The contributions made through your employer (whether by your employer or by you through payroll deduction or both) are reported with a code of 'W' in box 12 on your 1040. No part of this amount should be entered any place else on the return except on the W-2.
Contributions that you make directly to your HSA (not through your employer) are called "personal" contributions, although this term is very misleading, because many taxpayers think that their payroll deducted contributions are also personal contributions. Instead of "personal" use the word "direct" for these contributions.
The only thing that you enter on the second line of "Let's enter [name]'s HSA contributions" (see screenshot below) are any contributions you made directly to the HSA custodian. Note that the code W amount is on the first line and should not be repeated on the second line.
