Yeah, you'd have to have the elements on separate layers. I'm not a big fan of lens flares. It's one of those lower-intermediate techniques that, when a person learns to use them, they often go way overboard. One or two small well placed lens flares is far more effective than a whole bunch of big ones. They seem to be drawing attention away from the main graphics at this point, sitting right center as the brightest eyedraw in the image.
They may be conflicting visually with the gradients behind them, too. Try posting one without any lens flares, or maybe just the ones on the R and W, to see how folks like it.