Yes, it's pretty straightforward. But just to further clarify... you'll indicate your after-tax contribution on Form 1040, line 25 (health savings account deduction). The pre-tax contributions that were made through payroll deduction don't show up as a distinct line item on Form 1040 as they have already been subtracted from your W-2 wages.
On Form 8889, after-tax contributions will be entered on line 2. Pre-tax payroll contributions (both employer & employee, even though the description only says "employer contributions") are indicated on line 9.
So, assuming you are single and are therefore limited to $3350 in total contributions, if you make an additional $755 in after-tax contributions for 2016, you'd end up with the following entries:
1040, line 25: $755
8889, line 2: $755
8889, line 9: $2595
I am not a professional tax preparer, so don't take this as official tax advice, but I made the same mistake my first year with an HSA, not realizing the FICA tax benefit of payroll deduction. So my return from that year looks pretty similar to the example above. At least in your case, you're only out the Medicare tax of 1.45% on $755...or $10.95. :)