Your opponents will automatically target your characters and you can manually change the target if you have multiple opponents. Since you can change your battle order, make sure to place the character who is strong against the incoming attack. This is very important especially in boss battles.
The attack order is displayed in the lower portion of the battle screen. The order begins on the left and continues on to the right. You can change ther order of characters whose Ki Sphere path has not yet been chosen. Your opponents will target the characters closest to them who have attack. If your opponent's attack icon is displayed in the attack order, the characters closes to them will be attacked so place a character whose type is stronger than the attacker if you don't have any choice, place your character with the strongest defense instead.
The same goes when you're on the offensive. If there are multiple targets, consider targeting those weak against the attacking character's type. If a boss has minions, take out the minions first. To target a specific enemy, just tap on the target's portrait on the upper left corner of the screen.