Quartus II won't ever generate two programming files from one design. There are a number of issues(how do we know the pinout of the second device is the same as the first, and even if it is, which pins do we use? Transferring data between devices will add cycles/delays, which will change the functionality. Plus splitting a project at a given place generally adds a lot of other pins we would need to connect, etc.) These issues all need to be handled by the user, i.e. create two separate projects with separate code, and develop a way for them to talk to each other.