Where do I enter HSA contributions made in 2017 for tax year 2016?

You are in the correct data entry... you just need to continue until you are asked about the contributions. Once you enter 1099-SA information (if applicable), you will arrive at the summary screen. Keep on going. The program will eventually ask about the contributions (see pic).

1. Federal Taxes
2. Deductions & Credits
3. Scroll down to Medical and select HSA, MSA Contributions - follow the prompts; you will be asked about the contributions once you are done with 1099-SA

In this box, should we enter the amount we contribute in 2018 that goes towards the year 2017? or is this asking for contributions made only in 2017 for 2017.

I understand that we report contributions on 8889 Part I line 2 that we made during the tax year prior to 12/31/17, but where do we report any contribution amount made after 12/31/17 and prior to the 4/15/18 filing date? Do we add it to the 2018 contributions, is there a separate line for this or do we amend prior filing?

There is no distinction by date (ie, before or after calender year end). All after tax HSA contributions for a specified tax year go on line 2.

You do not add  2017 tax year contribution to 2018 tax year return.

If you forgot a 2017 amount, amend a 2017 tax return.

I forgot to report the extra $250 I was allowed on line 2 in 2017 filing. Probably not worth amending 17.