Number 3 is the flushing port
The SeaDoo flushing kit is worth the $12 or so. You can also screw a male x male water hose quick connect into the port with a female quick connect on your hose end. The male end of the waterhose will also screw right in but it is difficult.
Not sure about the other 2 ports.
Just always remember, start motor, start water, stop water, stop motor.