The order and placement on a ballot for the general election is rarely set earlier than a couple of months before the election (I don't have exact numbers for NC, but it sounds right). After all, NC just finished its primary runoffs a couple of weeks ago.
In South Carolina at least, the order was set well before the nominees were even established. For 2008 it will be:
Green
Republican
Libertarian
Petition
Democrat
Constitution
Working Families
Independence
With Labor probably added at the end since it's a newly registered party. (I'm not certain if it was added before or after the Independence Party was shuffled from the top to the bottom.) The order for 2010 will be the same as 2008 except that the Green Party will be moved from the top to the bottom. Assuming that these same parties all remain registered and that the regulations for ballot order are unchanged, the Democrats will next be at the top of the lists of candidates in the 2016 election cycle.