"1) Should box 1 have self-only checked? It says Check the box to indicate your coverage under a HDHP under 2021?" -
Yes. In fact, if you didn't have this checked, then you would get an error in the Federal Review, so leave it checked (no, it doesn't matter if it's Family or Self-only because you have indicated no HDHP coverage for any month).
"2) In box 2 it states : HSA contributions you made for 2021. My employer contributed X amount and I contributed X amount but through the employer. It states Do not include employer contributions ,contributions through a cafeteria plan etc. I'm assuming these would both fall under that category so the amount in this box should be 0?" -
Correct. The IRS call it "the employer contribution" on Line 9. This is the sum of everything your employer contributed and everything that you contributed through payroll deduction. The reason that this make a difference is that these contributions are reported in box 12 with a code of W on your W-2, and before your W-2 is printed, the code W amount is removed from Wages in boxes 1, 3, and 5. That is, you not only don't pay income tax on HSA contribution done in this way, but you don't pay Social Security or Medicare taxes either.
Line 2, the one you referred to, is the sum of any direct or "personal" HSA contributions that you made but not through your employer.
"3) There's a line 3 smart worksheet where it says select your coverage for each month below. I marked None for all the months. Is that the right thing for me to do? I was on a family LDHP until September. I joined my job in September during which I joined a HDHP from September. " -
Yes, this is the right thing to do. It would have been different if you were not a dependent, but you can look forward to tax benefits next year.
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