Unfortunately the cooling system on these 4 strokes is a complex maze. It is not a simple loop where the water comes in, cools the engine, and exits. There are branches and splits in the system for cooling various components. The best way to get an idea of how the system works is to trace the hoses that can be seen using the service manual where they enter and exit the engine and exhaust system. Much of the cooling system cannot be seen as it is running through water jackets around the cylinders, through the exhaust manifold, and inside the exhaust system. Look at the "Cables and Hoses" diagrams in the service manual.
If you really want to get an idea of how it works, get yourself a flashlight and the service manual and trace hoses. Remove the metal deck beam (4 bolts) so you can see down behind the engine area. Start at the cooling water inlet hose which enters the hull from the jet pump through the transom on the port side near the bottom of the transom. This hose is easy to find since it joins the flush hose at a "Y" joint, so you can just trace down the flush hose to the "Y" joint then trace the inlet hose to the engine. The service manual will show you the direction of water flow in the hoses. Cooling water enters the ski through 1 hose, but exits at at least 4 different locations. Once you have traced the entry point and the 4 exits and understand where the water came from for each point, you will have a pretty good understanding of how the system works.
