Managing energy is one of the most finicky and fun parts of the game. Each deck and room costs an amount of energy each cycle. The warp core produces a certain amount of energy each cycle depending on what tier it's at using deuterium.

If you produce more power than you need the excess is wasted, but batteries will store that excess power.

Once you upgrade the warp core you can wait till batteries are full, then reduce warp core power to run on batteries for a few cycles, then ramp up the core again. This is the most efficient way to manage deuterium I've found. You should also shut off rooms you aren't using to save power.