Is there away to control where ads appear in your game using Javascript. or is there a way to stop adverts from appearing in other scenes using C# without having to rebuilding my game from scratch using C#
I just found the answer to this myself. You need to move the GoogleMobileAds folder into the Standard Assets folder. You also need to move your script that creates the ads into the Standard Assets folder. You can then call functions in your admob script like you normally would.
Here is a link that explains why you need to do this.