PotatoBoiler
Alright, so at first there are the issues you already mentioned. Especially using compartments should become your new priority.
Second, what kind of ship is this, from what I see it tries to be everything at once. Try to create a ship which lets most weapons fire at the same time. Missile modules could be useful on the sides, so you can wreck them with a misssile barrage and railgun blasts at the same time. (Note: Small railguns at the flanks of your ship are a bad idea in most cases.)
You should also follow the advice we gave you on the previous ship for better powered shields and faster reloading cannons. (Actually, you don't really nead much shields on the sides if you are going to fill that place with missile modules, which would also remove the cannon ammunition issue)
Flak defense could be incredibly helpful on the front, you'll see.
With some improvements you should be able to beat this smaller ship of mine.
(Note: Your initial railgun strike does a lot of damage to this one, keeping them alive longer could already change the outcome of this battle.)
