I was like that too when I first went into a fortress, but I figured it out. You use a rune stone to start it, then you tap on the enemy to begin the battle.
Then it's like when you fight a dark type. You have to align with the three stars on the enemy to begin.
Next you have to find the circle on the enemy and stay there long enough so you can attack/trace once the circle is filled up.
Also you can get ingredients by walking your portkeys. I've found a lot of ingredients that way.