Best advice I can give is to simply start with basic shapes and then decorate.
Also, don't be afraid to put in blocks you know you're going to cut out later.
So say you're making a miner, start off with a bridge (as in, a room that lets you access your core), and then build your salvage array. Add in a simple box reactor around your array, and wrap a hull around it. You now typically have the classic flying shoebox or pringles can.
Look up at solarapple's detailed ship up there. Ignore the greebles and just look at the shape. Its a shoebox tacked onto the front of another shoebox. As in, the front half is a rectangular box sitting vertically, and its on a slightly larger rectangular box in the back sitting horizontally. Then he just added bulges to the sides, some piping and shapes here and there, and he had an interesting looking ship.
Thats how you do it. Build your ship as a basic shape. Add some lumps to it, then detail your lumps. You don't even have to plan it out ahead of time very much. Build your pringles can cylinder mining ship thats nothing but power and salvage arrays. You want some weapon arrays for it? Great, add some boxes to the sides to put them in. Need more room for shields or more power storage? Add a bigger section in the back to house it in.
Just keep doing that until your ship has everything you want, then start rounding off the corners with wedges. Then start adding some details like piping (which is just a fancy way of saying "drop some lines of blocks that serve no purpose other than to be lines of blocks that look like pipes"), cut some holes in the hull and then drop the hull level by one block in them so that you have recesses. Or do the opposite, add plates on top of the base hull to look like armor segments.
Don't try to build an uber-fancy ship from the start, because it'll bog you down until you don't know which way is up. Start with big simple shapes, then refine them down one step at a time. Don't be afraid to build shape segments that you know you'll completely redo simply to have them as placeholders so you can visualize the size and shape of that area for later. Big shapes refine into smaller shapes, smaller shapes get greebled ("greebles" being a movie model building term for decorations that only serve to break up large flat surfaces to make it more visually interesting).
It also helps if you sit down before you start building ships and come up with a "look" for all of your stuff. As in, figure out if you want to have a unified color scheme, and a uniform decoration style.
For example, the "look" my stuff has on my current server is Base Black, Red Armor, Grey Highlight, and Lava Power.
By that I mean I start all of my stuff in black. Black is the standard hull for everything (I usually use Black Standard Armor). Basic shape gets made out of this. Red Armor means I then go in and put red plates over things as if they were armor (usually just Red Standard Armor) to give them a look of being layered. Grey Highlight means my piping is generally Grey Standard Armor, the docking ports are grey, etc. Then the Lava Power is the final big unifying theme. I decided that I wanted my ships to have glowie parts, so I decided that my ships and stations are "powered" by lava. So they will have big open vats of lava, smaller vats of lava enclosed in glass or crystal armor, tubes of lava running between major parts, etc. Basically that my tech thematically stores power in hot lava the way Trek ships use plasma (remember, the EPS conduits are Electrified Plasma Systems).
That way, when I build a ship or station, not only do I keep everything looking like it belongs together, but I can flat out steal decoration ideas from one and paste them onto another and it makes them all look better instead of looking like I just re-used the same bits everywhere.
) And i want to ask the community, HOW THE HELL DO U GUYS MAKE SUCH DETAILED SHIPS! even the medium sizes look epic! Can someone give me a step-by-step guide on how to make medium -big sized ships? 
