Charms must be in your inventory to (permanently) inset them into equipment, not in the battle tower chest (you can use alchemy and enchantment ingredients from there, though).
In the PC version, right click on a piece of equipment with an open charm slot.
With the Xbox version, just select a piece of equipment with one or more empty charm slots in the inventory and hit A; in the equipment menu you can hit Y to add charms to equipped items (which is the only way to charm a bow in the Xbox version).
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