The other cells will only recharge on their own if not drained completely (as in from using abilities such as cloaking or heavy lifting, yet not using up an entire section of the battery in the process like a takedown would). Otherwise, only the first one charges on its own, and you would need the consumables to bring it back to full.
It seems questionable initially, but I'd say the game would be less balanced if the player could use up as much energy as they want, such as through spamming takedowns consecutively, and have all of it restore on its own (but then, abusing candy bars pretty much achieves the same effect).
