Martin's spot on (as usual) ::)
The best intakes are sloping tubes which can be flush giving the ultimate in low drag, or left a little angled for more flow (depending on what you're cooling. These were mine on a 3.5cc racer, one for the crankcase and head, the other for the manifold and pipe. You would only need the one. If you use 3mm tube, silicon water tube holds firmly (with a cable tie, of course).
Discharge over the side of the deck up near the motor, where you can see it when the boats kicking up some spray.
Transom corners which are dead square help keep the boat flat and create a clean break for the flow under the hull, thus reducing drag. With what you're sticking in there, sounds like you'll need all the control you can get
Good luck
Danny