in Turbotax it's taken care of automatically. the excess from the prior year is on the carryober worksheet.
the anount you enter on line 2 of the 8889 is only the actual amount contributed for the year excluding the prior year excess.
the 8889 is poorly designred becuase it it doesn't directly show the excess being utilized.
you'll see the last line (13) will say the smaller of line 2 which excludes the excess or line 12. however, the amount that appears on line 13 is the actual contribution (not in excess of line 12) plus any carryover utilized.
if you look at 5329 for the year you'll see line 42 report the prior year exess but then on line 43 any prior year excess is to extent utilized appears. lines 43 + 44 = line 45 this line is subtracted from the prior year excess and if the are equal there is no excess for the 6% penalty
