Objects in front of the prop tends to reduce their effectiveness. Props work best when they see clear air free from turbulence that occurs from parts of the model. So I vote for normal tractor use.
And yes, you will want to angle the motors so they face up by a good angle. On the flying boat I built last spring I went with +2.5° incidence in the wing and the motor pointed up another +2° more than the wing. It still had a slight tendency to dig in the nose when on the water during the slow part of the takeoff run. But in the air it was just about right. No strong tendency to climb with throttle.
I thought the prop was up high enough too. But the nose digging in even the amount it did caused water to come up around the nose and into the prop. So plans are to add on a pair of 1/4" (6mm) wide by 1/2" (12mm) tall extra chines on the nose both to aid with floatation in the nose as well as act like to direct the water more to the sides. I learned my lesson. LOTS Of flotation up front ! ! !
Bubbles original design flying boat.
Bubbles flying boat.