A hose goes from the waterbox fitting to the nipple on the left side of the exhaust pipe, note pic below,you are using a 650 pipe which does not have that fitting, look at the pics below the 750 pipe is longer in the mid section , it will fit in your ski,if you slide the pipe farther in to the waterbox and move the rubber boot up farther on the pipe body, but the exhaust coupler is larger and you would have to use the 750 exhaust manifold and head pipe.
Now that being said here is what you can do, drill and tap the stainless flange for a threaded fitting and run a hose to the waterbox fitting or you can just plug the fitting in the top of the box and go with it, what they are doing is diverting water from the pipe to the waterbox drying out the pipe in essence making the pipe even longer to work with the 750 porting.
You can also put a restrictor in the other hose to fool the pipe into thinking its longer