You have a Dream arts conning tower, don't you? The deck slots in the conning tower deck aren't open on those kits (the ones I've seen anyway).
Probably a silly question but you do have a vent in the conning tower, don't you? If not leave the main hatch open or off, this will ensure any air is vented from the boat.
Trapped air will cause you all kinds of headaches, as the air bubble will move around the hull and the boat will be in a different state of trim everytime.
Regarding your disappointment that the tank doesn't provide a scale waterline. Well you haven't wasted your money, a dynamic diver would require a considerable turn of speed to dive, you boat will be able to cruise along at a much more scale pace.
You could increase the size of your tank by ordering a longer tube and threaded rod from engel. Exisitng owners report you'll need 1L capacity to achieve scale waterline with the U47.
Andy