engine cooling

After storing my Sea Doo for winter I got it out of the shed last Saturday, put the battery and fresh plugs in the engine. Fired right up but was running funky... Loss of RPM's and when I hooked the hose up to the Intake the hull began to fill with water. Finally figured out the issue but need...

how does water flow from the exhaust into the head or engine for cooling purposes and then flow out the pee hole? any help understanding this would be appreciated