HSA Contributions: 6000 was pre-tax out my paycheck, and 750 was direct deposit from my bank account, but I have no box 12 W on my W2. What is my deduction? 6750 or 750?

Yes, as Lisa995 says, you need a corrected W-2 because normally the employer must enter your HSA contributions made through the employer on the W-2 in box 12 with a code of W. Your form 8889 won't print correctly without it.

As for the $750, this is your "personal" contribution. It will appear on line 12 of Schedule 1 (1040) as an adjustment to income. You enter this on the "Let's enter your HSA contributions" screen on the second line (see screenshot below).

Properly done, the $6,000 will be removed by your employer from Wages in boxes 1, 3, and 5 before your W-2 is printed. So, in a sense, it isn't a "deduction" because it was never in your income in the first place.

The only place that the $6,000 will appear on your return is on the 8889 on line 9. Do not enter this amount anywhere else on your return.

[Edited 3/26/2020 8:42 am CDT - updated for 2019]