In rear transom I have a port on both sides one for each engine looks like a flush port where I would connect a water hose , it has a rubber gasket like a water hose has.
Is there something that plugs that off while not in use and operating boat in the water ?
Yes... it's open. BUT... that's where some of your cooling water exits. The feed water comes from the pressure side of the pump.
Also... if you open your deck lid... you will see a "Perko" fitting on each side. (by the oil tank, and by the fan hole) Those are your flush ports. (normally)