How does a 2 disk game work? I am trying to put Star Ocean: the Second Story on my PSP.

I created a folder called Star Ocean and in that folder I have two other folders, Disk 1 and Disk 2. Each folder has the .bin file and the EBOOT files. Is the setup I have correct? Is the location of the save file going to matter (so it knows you should be starting up disk 2 once you are that far in the game?)