Awesome. I was gonna ask if you were making a ship with a huge exposed glowing weak point.
Well, like I said, it's exposed now, but you can see the bottom and top is already armored (I may add a second layer of hardened stuff, with slopes and more color), it's supposed to be the middle section that is going to be a bit saucer-ish. The cockpit will stick out the front, and a couple of doors to the sides will lead to some sort of utility rooms.
I've been reading a bit about component grouping, and this is more or less what I got: shields can be scattered all over and doesn't matter, power gen is better when you only have one block on each axis in each object, same for engines, but every extra separate engine loses like half a block worth of power. Then, you should only have one single big-ass battery, just splitting the same amount of blocks in two batteries can halve power cap. Guns have better DPS when they're tiny (single block is even better) but the range is better when grouping.
So, the inner powercube, I've filled all the empty space (minus the 6 "passages", up and down are mostly decorative) with batteries, and they all touch each other.
EDIT: Sooo... I covered the central part with a saucer (looks more like a hamburger, or something) and now it's really heavy and cumbersome (maybe I should have left it hollow instead of filling it completely with shieldgens?). Anyway, here it is:
I think my basic mistake was not putting the engines last. I'll probably end up replacing the single engine by two 90 degrees rotated clones, side by side. And/or add external nacelles to the design.