Well, for a start avoid giant brick shapes (or the shapes offered in th build helper for that matter until such a time as you feel more comfortable with your output).
Second, as you only want it to look better, I can presume you are happy with the systems?
- If so, save a BP.
- Exit the game and EXPORT the BP (very important!!!).
- In SP mode find the BP in the catalogue (NOT the export - that thing is for backup).
- Purchase.
- Fill.
- DELETE THE BP FROM THE IN GAME CATALOGUE!!!
- Now... ensuring you ARE NOT in creative mode, spawn the BP and collect the blocks.
- Rebuild the ship systems first - doing your best to vaguely emulate a ship shape you like that sisnt a cube. Then put the hull on sparingly.
- It wont look amazing to begin with, but you will have systems you're somewhat happy with, and something to build upon visually, rather than what you credit as efficient systems and just covering it with hull.
Consider it a bit like making a lego house according to intructions, but finding a better house to make from those same pieces. I'd go deeper into the theory, but its something often utilised by designers, artists musicians and writers: "...all you need are the bones of the thing. The flesh is weak and can be made appeasing".
[bonus marks for the person who can find the famous quoter of that remark]
Of course, this method may not well work for you immediately, but is a good way to begin finding a style you like to build in, and a good excercise for the mind in anything similar. Hope thats of help.