Your reactor is the second-most important item in the game, second only to control rooms. I will be your guide in designing ships that have great defenses for reactors.
1. Center your ships around it.
This will help you when you are starting out. Your entire ship will have to be destroyed for your reactor to be blown up. This will help out when you have little to no weaponry, but you can power it relatively easily.
2. Surround your reactors in 1 layer of armor at least.
This will help when you are designing long lasting ships. Surround you reactor with 1 layer or more of armor, then add a couple walkways to it. This will help with armor-penetration weaponry, such as the Railgun and Cannons.
3. Have easy access to corridors and Moving walkways. This will make it faster for your ship to charge up,and be kept charged. this will also help with shielding and laser weaponry.
4. Never let it be behind outer areas of your ship.
This includes weaponry, shields, and engines. This way if you gets shot by a railgun or cannon, your reactor will be safer.
5. Have Power Storage do some of the work.
Having shields means that you will constantly be draining an important reactor. Instead, put some Power Storage behind them, and Ion beams.
6. Have your reactor close to crew.
Doing this will allow things to be recharged even faster.
These are some of 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