The Soul in a bottle is an item used for dungeon making, boss fighting, and mercenary carrying.
Left-click a mob to store it in the Jar, and then right-click the ground to spawn it again.
The NPCs will sometimes sell jars with mobs already in them, like rare bosses or mercenaries.
If the Mercenary Controller is used to make a mob be a party leader, when that mob is put into a Soul in a Jar, all the other things in its party will also enter the jar.
SIAJes are also used with npcs to spawn monsters in certain events.