How much higher is the deck than the thru hulls? as long as the deck is higher than the thru hulls the deck will still drain even if the thru hulls are at or below the water line as long as the deck is above the water line. If the thru hulls end up at or below the water line I'd recommend you install check valves in the hose between the drains and the thru hulls. I don't know much about that particular hull.
Where is the battery (batteries?) on the XScape? If it's in the rear - just move it up forward (under a seat or something) and it should make up for the extra motor weight.