How I build a ship depends to a large degree on how large it is and if it will make use of medium to large turrets. My turrets are nested ball turrets, which take up a lot of room inside the ship. They look deceptively small on the outside, but pack a huge wallop compared to similarly sized turrets that are not nested ball turrets.
If the ship is such that it will not use such turrets, typically anything under 10K mass, it's shape will be primarily determined by the power structure I use for power generation. There are a number of options for such power lines and I will pick one based loosely on how I want it's final shape to be. Often however, I will have little idea what the final ship will look like until I am very close to finishing it.
For large ships using turrets, power is less of an issue. They are large enough that one of my standard power structures will fit somewhere along the length, height and breadth of the ship sufficient to generate maximum power regardless. In that case, my ship planning always starts with me laying out the turret placement on a wire frame. I want turrets to have clear fields of fire, for them to not obstruct one another and be minimally obstructed by other parts of the ship. While wireframing, I will also box other any other critical interior and exterior elements so I'll know they will fit and what impact they might have on the ship's shape and function. By doing all this in wireframe before hand, I can eliminate most issues that would otherwise force a complete redo.
Once I am satisfied with the wireframe, if the core was not already properly placed, I will redo the wireframe with the core placed exactly. Typically I will actually install the turrets first thing, as the ship will quite literally be built around the turrets. Then if I am intending any interior I will usually build the bridge first, then any essential passages and rooms so I don't inadvertently mess up an area I will likely see frequently. Then I will install any mission critical elements that take precedence over any aesthetic concerns.
From that point, I will normally wedge the exterior hull so I know what space I have on the inside and then proceed to fill the inside (any not used up by interior spaces anyway) with systems such as shields, thrusters, etc. Once it is fully wedged, I will give it a once over to see if there is anything I can add to the exterior that will increase either it's functionality or it's combat performance. Frequently at this point I will figure out several places where I could add additional point defense turrets, and I will make whatever changes are necessary to do so.
I will also make a tiny concession to cosmetics here and see if there aren't at least a few tiny touches that could not be made to give a ship a bit more color or texture. As little as a single line of complimentary color can make a real difference to the visual impact of a ship. I typically do very little greebling. (Greebling is adding decorative features and textures that have no bearing on functionality or combat, and exist solely to make the ship visually more interesting.) I personally do not find such greebling attractive, I find most ships use WAY too much of it. I like my ships showing what they do, sheer functional efficiency in all domains, be it civil or military.