Your control room IS THE most important item in the game. I will be your guide in designing ships that have great defenses for Control rooms.
1. Make sure to have it Armored.
If you don't do this, you might as well kiss your ship goodbye. Armor around this part increases your survivability bit by bit.
2. Never leave it outside your ship.
While yes, some ships have it outside of their main body, DON'T do this. If you do this later game, you are asking for an Ion beam or Railgun to saw it off. Instead, make sure it is more internally made into your ship.
3. Have multiples of them.
Having multiple Control rooms on big ships is really good. On small ships, it won't work because it is already extremely hard to armor with one control room. On big ships however, It is great because the enemy will have to literally cut you in half just to reach them.
4. Never have them near ANYTHING that goes boom.
The reason being? Explosive Parts (A.K.A. Factories, Reactors, and Some Storages) Will explode if taking too much damage. Having any of these parts near your control room is like putting a target there.
These are the basics of what you need to know. If you have any questions, I will answer them to the best of my ability. Go to this post for more tips. https://forum.cosmoteer.net/d/4578-dos-and-don-ts-for-building