To put a lens flare on its own layer, fill the layer with black, then, on the layers panel, change the mode of that layer to 'screen' and then place your flare. If you want to be sure the flare goes exactly where you want it, you can also mark a place on the black layer (a very small circle/dot of white -- or whatever color you want, just make it small). As I recall, the Apple version of PS let's you place the flare (if you're using the PS filter and not some other plugin) at an exact location by noting the spot on the navigation/info pallette whereas the PC version does not do this.