Personally, I've experienced that using the healing Ki move (hold down L3), which not only refills health but restores lost health bar, seems to be what you're supposed to do before a boss/at boss checkpoints if you go into it with any Ki available. Rather than saving it for Ninpo.
Some boss checkpoints make that a bit impractical, but for example against the day 03 dino, I was able to recharge a decent chunk of my health during the startup and still dodge out of the way when he charged me. Well that, and you could charge up Ki during the fight, and recharge while Derpasaurus is currently knocked out against a wall.
And the final checkpoint for the day 04 boss starts you off in the room before her final stage so you can easily pause and recharge if you've got the Ki.
Combined with a few other moves that actually use up Ki in this version, like bullet time bow targeting in the air, makes me think that Ki management and thinking ahead before blowing Ninpo on a group of enemies, is primary to attacking stages strategically.