There is one large compartment, this has the padded case which you can change the position so its in the middle (creating 3 compartments) or you can put it to one side (creating a big compartment and the padded compartment.) There is also another smaller compartment at the front of the bag which is fantastic for holding goggles and is very rigid so protects stuff.
I have one of these kitbags and it gets crammed in the car with loads of other stuff and everything is always well protected. I wouldnt swap it for anything else.