Ok, sorry for my being short on explanations, I'll make up for it right now.
First, just a tiny bit of theory: for any given RGB image in Photoshop we can build exactly the same image, but composed of four layers: the bottom layer - just solid black layer. And above it three solid color layers with Screen blend mode - Red one, Green one and Blue one. For each of these color layers we create the layer mask and fill it with the contents of the corresponding source image channel, that is: on the Red layer mask we paste the source image Red channel, for Green layer mask - source image Green channel, and for Blue layer mask - source image's Blue channel.
This way we can make image where pimary color layers play the role of channels in any image.
In your case we need just that(except for bottom black layer):
Make a new document. Create new layer, fill it with black. Go to Filter->Render->Lens Flare and apply the flare you want.
Now load Red channel as a selection(just press Ctrl-Alt-3) and with the selection active create new Solid Color layer. For it's color choose pure Red - (255,0,0). Turn this layer off.
Load Green channel as a selection(Ctrl-Alt-4) and with the selection active create Solid Color layer with the Green color - (0,255,0). Turn this layer off too.
And, finally, load Blue channel as a selection(Ctrl-Alt-5) and with the selection active create Blue -(0,0,255) Solid Color layer.
Turn on the Red, Green and Blue color layers we just made and set Screen blend mode for each of them.
Select all these three color layers(in old PS - link them) and merge selected(Ctrl-e). For the resulting merged layer again set the Screen blend mode.
The black layer with the Flare filter applied can now be safely trashed we don't need it any more.
So, here we are! You got Lens Flare on it's own layer with transparency.
And yes! You can clone stamp it on any transparent layer in Screen mode and put them flares as many and wherever you want. And you can apply Layer Styles or any adjustments to it. And much more...