Using Reactor Energy in Trigon: Space Story is about balancing what you should need in every situation. Never turn off your shield generator or life support module, and instead work around the other systems.
Where to focus Reactor energy in Trigon: Space Story
When in battle, only turn on the specific systems you need. For example, keep the Medbay, Stealth System, Teleporter, and Drone Control Module off until you want to use them. They consume Reactor Energy, and you don't need all three in every battle. Spend most of your reactor energy on your Armory Module.
The more energy you have in your Armory Module, the more damage you are able to give. The three main systems you should use during battle are the Hyperdrive, Shield Generator, and Armory Module. If you are out of battle, you can switch on your Medbay and focus a lot of your energy on Life Support to keep your crew supplied.
Pause a lot in battles and refocus your energy when you need to do something big, like activate your teleporter or stealth system. Don't worry about the systems on the right side of your ship. These cannot be disabled or enabled, and they do not affect your reactor energy. The systems on the right side of your ship are very cheap to upgrade on Stations, so feel free to upgrade them without worrying about losing reactor energy.
For more on Trigon: Space Story, check out What's the difference between Trigon: Space Story and FTL? or Is there multiplayer or co-op in Trigon: Space Story? here on Pro Game Guides.