The 3 empty slots at the bottom are power-ups you can hold by buying them before the match with gold (on the right side of the screen before the match in the game chamber). You just click to buy them if you have the gold.
In battle the power-ups on the right side you can use whenever if you click on them. However each one has a fatigue cost so you may only use so many per turn.
I hope this answered your question.
edit: my apprentice beat me to the answer. GO APPRENTICE RIRI!!!