On my form 8889, Line 2 says 0 and Line 9 has the amount I personally had deducted from my paycheck into my HSA. My employer does not contribute any funds to my account.

Line 2 is your personal contributions to your HSA. Line 9 is the employer's contribution.

That seems obvious except that these terms don't mean what you would think they mean.

This is IRS terminology, which TurboTax has to follow.

The IRS calls the sum of the employer contributions and your contributions through a payroll deduction plan to be "employer contributions".

It's counter-intuitive, but the reason is because this sum (which is reported in box 12 with a code "W" on your W-2) is treated one way - both amounts are pre-tax, and the employer places both amounts into the HSA. Another way to look at it is that you and your employer negotiated a payroll deduction plan, so that the employer paid part of your salary to the HSA in return for you not having to pay tax on it.

This is as opposed to amounts that you might contribute to your HSA independent of your employer (which is possible).

So the way form 8889 is completed is correct.

My W2 line 12 code W shows $3500, but my personal contribution to HSA is actually $3485 and employer $0, should I  still enter $0 for form 8889-T line 2 and let line 9 show the number ($3500) from W2? Also confused about line 3 smart worksheet, I'm single and have HSA only for myself, should I not checking any boxes on A1-A12 to have all monthly contributions be $0 in my case?