You have two options.
The safe option is to save the game at the end of one disc. As far as I know, every game that spans multiple discs prompts you to save your game at the end of every disc. Save your game, then exit the emulator, then unmount the first disc and mount the second one, restart the emulator and load your save.
The fast way (but I think it doesn't work for Chankast, but I may be wrong) is to unmount the first and mount the second without exiting at all the emulator at the "Insert disc X" screen. After the second image is loaded, press start or A (or whatever) and continue playing.
You can experiment yourself with combinations of the above and tell us what you got. It might help the authors find potential problems in the emulator (even though Chankast seems to be not in progress).