The section you want is under deductions (not healthcare). Look for HSA/MSA Contributions.
Form 8889 is the HSA reporting form. It has three parts. Your contributions will be in part I.
The program will ask if you had excess in 2015; you will answer YES, then enter the amount ($57). The $3350 should come in automatically from you Form W2 (box 12, code W). The program will also ask about HDHP coverage. You will be required to fill out a table indicating the months you were covered by HDHP. In your case it will be 10 months. The program will calculate the limit of $2791.67 and see that there is excess. You will be asked if you withdrew excess. Assuming you do this before April filing date 2017, answer yes and put in the amount (even if less than the actual excess). I haven't been through this process as yet for 2016 but this is basically how it has worked in the past. BE Aware that the program is still being updated frequently so you may find that some sections are not full function.
