With the Futaba system as long as the antennas are above the waterline orientation doesn't seem to be that important, I usually tape mine to the underside of the deck if I can manage a 90 degree divergence, so much the better but range is not an issue - 470+ yards and still going fine.
With the Spektrum system however, I have found it alittle more 'fussy'. Best range is achieved when with the AR6200 twin receiver setup, one receiver is oriented vertically, and the other oriented horizontally along the length of the boat, usually in my case the main receiver is attached to the underside of the deck horizontally, with the satellite receiver mounted vertically in a deck cabin if possible, else attached to the combing. Usefully, you can buy extension leads for the inter-receiver lead, in my 1/24 PT Boat I'm using an 18" lead to mount the main receiver 6" from the stern with the other satellite mounted behind the model instrument panel on the bridge another 14 inches further up the boat.
I add again that these are my findings over exhaustive testing - I have no life (!) Both systems are more than effective WAY beyond usable visual range.
-Rob