The children go from having separate classes according to age group, though all taught by Miss Hunter, to all being in the same classroom together. In Season 1's The Star, Ben is shown having Miss Hunter give a spelling bee that only Elizabeth knows about until after it is over. Also in Season 1, in The Fire, John-Boy and Jason are shown having a science class, also taught by Miss Hunter, with only students of high school age. After the building is burned to the ground, she goes to Ike Godsey's store to find a classroom for the older high school students. She says she has found alternative classrooms for all of the other students except for the older ones. Now she is suddenly the teacher for children of all ages in the same classroom.
It's unlikely that the school board would have to resort to hiring a substitute teacher all the way from New York, as opposed to the much closer urban centers of Richmond or Charlottesville. Likewise for Megan, if she was searching for a teaching opportunity there would no doubt be opportunities closer to home in New York rather than having to accept a position 400 miles away in Waltons Mountain.