Switching disc

I have an emulator called EmuBox and i've been playing Chrono Cross (which is 2 discs). Well it doesn't give you the option of saving right at the disc change... I've been using the in game save instead of saving with the emulator. If I open disc 2 and load my last save it tells me to insert disc 1. Ive even tried saving with the emulator right at the "insert disc 2" screen. But when I try to open disc 2 it won't let me load it that way because its for disc 1..... I cant find anything on this app online... Anyone have any ideas of what I can do so I can continue playing?