After a lot of trial and error, tutorials and trouble shooting I managed to get my first FMOD & Unity integration project working using the Space Shooter complete project from the Unity Asset Store.
The Space Shooter complete project comes with sound already in game using the Unity audio engine. The sounds are all basically one shot samples added to game objects via Unity Audio Source components. I could have just replaced each audio file with a new one of the same name, but I wanted to implement the sound with FMOD and take advantage of things like multi sound modules and pitch randomisation. This meant I had to replace