In this world FTL travel is accomplished by entering an alternate dimension, let's call Aqua. Aqua is a very simple, albeit strange dimension. A great expanse of water as far as civilization has mapped stretches out, dotted with islands, and an ocean floor. Not a planet, just a strange expanse of water. 

Different locations along an X-Y plane in Aqua correspond to specific locations along an X-Y-Z space in the main (normal) dimension. The center-of-mass of the object exiting Aqua has to be roughly (only roughly) sea level, and likewise an object entering Aqua always enters roughly sea level. This allows trips of thousands of light years in the main dimension to be reduced to simple months of travel in Aqua.

Gates can be opened up between the main dimension and Aqua, and the gates are designed to hold the water and atmosphere back, creating a barrier for the water. Gates can only be made sufficiently removed from gravity wells, thus being limited to space.

How Aqua works, as how the jumps to and from aqua work, and the general nature of Aqua are all outside the scope of this question, unless they'd affect the design requested at the end of this post. Consider it all handwavium.

What *is* within the scope of this question is what the vessels would be constructed like: this is a question about design.

Points of consideration:

* Movement in Aqua: Floating like boats? Submarines? Like aircraft?
* Vessels need to be designed for the lack-of-atmosphere in space to the pressures of Aqua (similar to Earth's)
* Vessels need to be designed to be able to accelerate/travel in both space and Aqua.
* Trade transports should be constructed as economical as possible.
* Space military vessels need to be able to protect themselves or be protected in a sensible fashion both in space (obviously), and in Aqua. Military vessels might be carriers, transports, or vessels meant for direct combat.

...What would be a sensible design for these vessels?