Our middle and senior youth group meet only at second hour. We have junior and senior high classes both hours, but wish we had done more preparation with youth parents in consulting their youth about choosing an hour. Most parents accepted it with a little explanation of our options. We tried having students at all three hours, but the kids simply gravitated back to the middle hour, and parents were OK with it. The fellowship time between Bible studies works great with singles.
Youth do tend to go back and fourth forth between hours.
It takes a lot of work with the parents to make two hours of youth Sunday School work. We're going to two Sunday Schools this fall. We developed the plan nine months out, shortly after I came on the field. It included every group and leadership entity that we could identify in the church. It also included surveys, announcements, dramas, sermons and anything else we could dream up to do the job.