Opacity=is how bright your colors are and how much light can pass through the layer. 50% Opacity will make the layer transparent.
Fill=is the density. With 50% fill, you will be able to see through the image, BUT if you have any effects (shadow, outter/inner glow, etc) they will be visible at the percentage of your opacity.
Example.
IF you want to make a screen. Opacity should be 100% so the screen has the inner shadow,stroke, and whatever effects you want to add. Set fill to 50-40% so it will become glass like material.
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