So far I haven't done anything to big, and I hardly decorated my ships. I did notice that with the smaller ships I end up making a few versions, just because it is so easy to start over with the general design.
With most of the things I do that require any significant amount of effort is to first think of what I want in general, then visualise it better in some way, and if that isn't clear enough I use a different method to make it easier to understand/read/visualise, and this step gets repeated whenever I deem it necessary. Once I've got the rough sketch done, and once I worked out the details in some way, I start working on it in its original form.
With my rectangular cubed salvage ship: I used starmade as visualisation tool. I made a general design, tested, removed/deleted, started over. This continued for a while until I had my final ship, after which I realised that it was fine for what I wanted, looked fine and stopped working on it (I wasn't really into ship designing back then, but I am now).
For creating custom crafting systems: I first write some details, but mostly general information, on paper. It is simple to use, can become a bit, well, "not easy to use", but that's what the next step is for. So the next step was putting all the details in excel (very easy program to use for this task). I put all the general resources used for making each block in it, and I put all the general information on paper again. Finally I used the block editor to change the recipes.
I suppose that if I were to make a bigger ship I'd draw something outside of starmade first, and then I'd loom up tutorials on how to design a ship :p
The next ship I'm going to make isn't going to be big, so I'll just use starmade to visualise everything. I'm basically just going to use the same method I used for my rectangular salvage ship (which had 625 salvage beams, and it was actually quite cool; it had lasers!).
Oh yes, my ship is going to be a modular one with different tools that can be equiped to acheive different tasks.