Just like any other ride, you can get in line for HE until park closing of the park that closes first. Then it continues to run until everyone is through the line. Both parks closed at the same time but I entered the HE like about 10 minutes before the parks closed and they let me know USF would be closed by the time we'd get there. I ended up missing just the first little bit of Cinimagic Spectacular.
HHN have been different where they want to clear the park quickly.