I may be wrong, but there should be a draw or some kind of tiebreaker to determine who is conference champs. Whomever that is would be a top seed in whichever bracket they are in. They wouldn't get two top seeds ie: one in 1-A and another in 1-AA. So if North Duplin wins the tiebreaker and are declared conference champs for seeding purposes they would be a top seed in 1-A, but if they lose the tiebreaker, then they become a wildcard team and would be seeded by record only!
From a reliable source, with ND being a CoChampion of the Carolina Conference they will get a #1 seed in 1a for being the only 1a team in 3 way tie. Lakewood will get the #1 seed in 1aa due to defeating Princeton in regular season and Princeton will be seeded by win/loss record. All three will always be 2016 CoChamps in record book.