Well some of the ship designs especially the ones in the library are simply 3d models that have been imported into the game but I too have seen some extremely impressive designs made in the ingame designer.

I'm not one of the uber ship designers but I probably spend as much time designing as playing.
I usually start with a prefab hull because I like having some base to work off of but I have used the cubes on occasion. The biggest piece of advice I can give is to take some time to get to know the ship jewelry. Their are many pieces that I never use and several that I almost always use. I have had enough practice that when I decide to go for a particular look I usually have an idea of what piece I want and where it is.

Another piece of advice is to use Kryo's Hull mod. You can't use it for metaverse games but it is very nice. It adds all of the ship hulls from every civ to the jewelry so that you can create some very interesting designs.

Hope this helps,
Tral