I guess somewhere along the line I thought that I needed a solid black layer to put the lens flare on and the solid green was for the green colour.
I will totally try keying out the blacks in the flare. That sounds like it might work (I knew I was missing something)!
I guess maybe another way to go about it just add a lens flare and make it green.
So maybe my real question is how do I superimpose a lens flare and change the colour so that only the lens flare is green?