1. What Do I Need? - I typically start off with coming up with a role that I need filled, as it generally impacts how my final ships will look. For example, I'm soon going to start working on an antifighter ship. It's going to be a relatively simple shape to give the turrets as large a sight line as possible around the ship.
2. Testing - I then start out with testing different weapons. Being still a novice at weapons, I try to just balance power requirements, and look to the forums for help. For my anti-fighter ship, I built the turrets that will be mounted first, and tested them on a power block to see how much power they are draining, and spawned in a couple swarms of fighters to see how well they do at taking them out. For my Hippogryph, I wanted strong missiles to take out hull, while still having a lot of them launching to try and get through AMS defenses, and still not draining all my power. Since I built the missile groups 14x2x2, the missile pods/shoulders ended up making the ship look fairly beefy.
3. Concepting - After I have the turrets and weapons mostly figured out, I start concepting. I make a very small ship, less than 30 blocks in length, and start defining the general silhouette that the ship will have, and marking areas where turrets and weapons groups will be.
4. Wireframe - Once I have the general shape worked out, I size it up. Usually this involves deciding on how long I want the ship to be to fit weapons and whatnot. For example, my antifighter ship will have turrets in groups of 3, with 2 groups going lengthwise. Each turret is 17 blocks wide, and I want room to make it look good, so the ship will be 17blocks*6*2 = 204 blocks long, giving my ample room to have the turrets and make them looks proportionate to the rest of the ship. I use that number to build the wireframe, giving me a VERY LOOSE space to build in. I emphasized loose because I don't want to get locked into making sure it is that exact space with no room for future ideas or streamlining. Here is a picture of my Orthos concept ship compared to its wireframe:
https://goo.gl/photos/LaJRDP7WjcU9SKCM8
https://goo.gl/photos/LaJRDP7WjcU9SKCM8
5. Building - It's here where I actually start detailing. Unlike a lot of others, I don't have a general building phase and a detailing phase. I typically do both at the same time. This ends up with parts of my ship looking completely done, while others aren't even started, as seen here:
https://goo.gl/photos/xz5u2hCf3cmTgJQ56 I may hop around the ship a bit, building parts that I know what I want, and then stitching them together at the end. Of course, I can still go back and change things if I want to, as what happened with my Hippogryph. While building, my style involves using large armor panels to define the general shape of the ship, and industrial greebling to give it some dimension underneath that armor.
6. Interior - I do the interior next, fleshing out what rooms I want, separating them into decks, and generally making it looks nice. Not much needs to be said.
7. Systems - Finally I do the systems. Again, not much needs to be said.
TL;DR Come up with stuff on my own based on the role it needs filled, create small ship for the shape, make a bigger version, build from there.