There's "Swap disc" option , but I don't have any game's saves right before a swap point to test that feature.
maybe the save files could be found on the net (I know parasite eve is one of them, I could test it).
Edit :
It could be tested another way :
load Disc2 and select Start new game.
It will ask for disc 1, swapp, win
I'll rip some games to test.
Edit :
Tested with Chrono Cross.
Starting a new game on CD2 asks for CD1, but after choosing the 2nd Iso, it can't go back to the game.
I don't know if it's only a problem with Chrono cross, or with the emu config maybe.