OH. I understand your problem now XD XD haha. Sorry.
Okay, let's say you have a layer:
Layer 2: Large Red Square
Layer 1: Small White Circle
The Large square would cover over the white circle, obviously...
I would just rearrange the layers, to:
Layer 1: Small Circle
Layer 2: Large Square
If you can't do that for whatever reason and you want to do a selection---get the magic wand out, hit Contiguous and "Sample all Layers" Set the tolerance to a good level (you can alter it if the default one doesn't work out for you)... select all the areas around the circle, then do the fill on another layer.
Also, next time please just ask photoshop questions on my photoshop tutorials page! please. Unless it's a specific effect you see in the comic page