Well, right now, I have only one bit of advice, and that deals with weapons on an attack sub. I will conduct further experiments, but the deepest a missile can go if mounted on pylon (in SimplePlanes of course) is 59 ft. I know, its a very shallow depth for a nuclear attack submarine, but oh well. Right now, I have no idea how to bypass that.
On iOS, the deepest that a missile can be launched at is sea level. If it even touches the water for a second and is lifted back out instantly, it will be unable to take off.