For charms, with the Xbox version, just select a piece of equipment with one or more empty charm slots in the inventory and hit A; a menu will come up allowing you to permanently charm the item with any of the charms you have collected. In the equipment menu you can hit Y to add charms to equipped items.
On the PC right click a piece of equipment with an empty charm slot.
For gems, you will need to find enchantment formulas and an enchanter. The enchanter can also remove enchantments on equipment you have, which will give you the formula if you don't already have it (you don't recover the ingredients, though).
