Personally I'd say prioritize acquiring upgrade stones and enchants over rushing to upgrade your spells, with a couple of health upgrades and some basic enchants, I think you'll find them a lot less threatening.
I say this because the, or at least my general tactic for fighting Shadow Bats is just running in a circle, they hit hard but they are pretty stupid as long as you can manage to jump over them when they come near you they aren't much of a problem.
As an incidental point assuming you have already died in the boss room don't even bother trying to go back, it's just asking for trouble, as you will have to fight a vengeful ghost as well as the Shadow Bats