ManaStoneContainer, ManaStoneTile, and ManaStoneScreen are not blocks and should not be in your blocks package. They should be in inventory, tileentities, and client.gui respectively.
https://github.com/Cleardragonf/AsuraMagica/blob/master/src/main/java/me/asuramagica/blocks/Mana_StoneTile.java#L101-L103
BlockPos.getInBox(...)
https://github.com/Cleardragonf/AsuraMagica/blob/master/src/main/java/me/asuramagica/blocks/Mana_StoneTile.java#L150
1) you can just make the field a CustomEnergyStorage in the first place so you don't need to cast
2) you shouldn't have "add fire energy" as a separate method from "add water energy" on your custom energy storage as you already separate them by using different instances
3) What, if you're "adding fire energy" as your singular method name, its named wrong.
And now on to your requested problem
https://github.com/Cleardragonf/AsuraMagica/blob/master/src/main/java/me/asuramagica/blocks/Mana_StoneTile.java#L249
Because all of your energies are all the same ENERGY capability you can't distinguish which energy you return from GetCapability.
Either:
1) make a new capability
2) use a custom energy storage that stores all four as independent variables
I recommend #1, as #2 will require an assumption when dealing with energy systems from other mods (which one is the right type to send over?)