Noah attacks automatically when he is close to enemy animals (the ones with health numbers over their heads). You can also right click to cast a spell every so often (designated by if the little circle to Noah's too right is full dark blue or not, roughly 10 seconds I think) that hits a radius around where you click at. 

The friendly animals that fight for you come out of the spawners (nests and dens) that you place around in the setup phase that happens before each wave starts. 

Thanks so much! Yeah putting in the endangered animals that you can save and put on the Ark idea came to me like the night before submitting lol

Glad that you enjoyed the game!