I build alot of original ships... What I do is first decide what the ship is for, and how the basic physics of the universe work.. IE, FTL drives, sub lights stuff like that, that will help to determine how much mass you need and how big things should be... Like EG said, it takes some math... Next I draw some basic shapes out to get where I like it... then I draw out some detailed side views to the scales based on the math... but I always draw out a scale box first so I know what 2 meters looks like. When I get the general dimensions and the general flow of the design worked out on paper, I start the 3d scaffold. I draw out a 2 meter tall by 1 meter wide by 1 meter deep scale box. Then work out from that the basic dimensions based on my side view sketches... Is this the best way to do it... I don't know.. but it's how I do it.... just make sure that you use your scale box, and match it up against your details and such as you build.
Here you can see a side view sketch of what would become the victory class... notice the scale box by the bridge...
Here you can see the basic shape coming along and the scale box.
Here you can see details starting to take shape.
Here is a shot further up the spine of the ship... You can see I have created a copy of my scale box and am using it in scene to match the detail scale with the rest of the ship.
