Deductions & credits

What I did was start playing with the program early.  I'm still waiting for the official W2 and other forms of course.  I'm in no huge hurry to file this year.  So far, the only place I can find in last years return is on form 8889 where I reported that I withdrew the excess $57, I'm still not sure if I did that right?  I know I correctly left the W2 block as $3407, I did not change it to $3350 or play any games that way.  So are you saying I would withdraw the remaining balance of $388 and take the penalty on the rest of the $558-388 = $170 ?