Create a new layer and fill it with 50% gray. Put your Lens Flare on this layer (Filter > Render > Lens Flare). Set the blend mode to Hard Light. The gray will disappear and you'll be left with just the lens flare on its own layer which can be repositioned using the move tool.
Related Resources:
Photoshop Filter Techniques
Compatibility: Photoshop 5 and higher, Photoshop Elements
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