First, to account for the HSA contribution that was not reported on your W-2, use the following steps:
- Go to the Deductions & Credits section
- Scroll down to the HSA, MSA section
- Click Start or Update
- Be sure to check the box that you have an HSA account
- Go through the screens asking about receiving Form 1099-SA reporting distributions
- Next, you will be asked about contributions that were made to your HSA, either by you or through payroll deductions
As you go through the screens asking about contributions to the HSA, there will be a page with the title Did your employer tell you about any other contributions? The third box on this page labeled Employer and payroll contributions not reported in Box 12 of your W-2 is the appropriate place to report your contribution.
Next, since you and your spouse are both covered by an HDHP with an HSA, even though one of you has a Family plan and the other has a Self-Only plan, for the purposes of the contribution limits, you are both considered to have Family coverage. That will increase the total contribution limit available to you.
From the IRS Publication 969 Health Savings Accounts and Other Tax-Favored Health Plans,
"If either spouse has family HDHP coverage, both spouses are treated as having family HDHP coverage. If each spouse has family coverage under a separate plan, the contribution limit for 2024 is $8,300."
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