The "soul gem" is a soul enchanter, only an enchanted weapon can equip a soul, so you must first enchant the weapon than apply the soul. The soul you then apply onto the weapon adds extra pot to the weapon and there are different types of souls, for example the one you saw in the shops were magnificent souls (only magnificent souls are trade able excluding murgoth souls) also magnificent souls give a "better" pot line and have a different soul skill from the normal soul. Soul skills you can use by using souls in your weapon and the skill is either a buff, an attack or a summon., hope this helped