Do you have a code W in box 12 on your W-2? Is it the $2,000? If so, this represents the "employer contribution", which is the sum of what your employer contributed PLUS what you contributed by means of payroll deduction. In this case, the $2,000 would indeed belong on line 9 of the 8889.
Form 1099-SA reports on distributions from your HSA, not contributions to it.
If there is not a code W in box 12 on your W-2 or if you and your employer did not contribute $2,000 together to your HSA, then it might be a good idea to write down what's on your W-2, delete it (use the Delete button or the trashcan icon) and then re-add it manually. This means Continuing past the screen in the W-2 interview that asks for the employer's EIN to the next screen where you enter all the data on the W-2.
If you received a form 1099-SA, then you would enter this in the HSA interview (do a Search for hsa (lower case) and jump to it).