When you're customizing layered Photoshop files, the preserve transparency option comes in very handy. The Preserve Transparency option allows you to make edits only to the visible contents of a layer. When the Preserve Transparency option is on, any transparent portion of a layer will be preserved. For example, if you apply a fill to a layer, only the non-tranparent portions of the layer will be filled.
If you're taking the time to roll your mouse all the way up to the little Preserve Transparency option in the Layers palette, you're probably killing time. Get in the habit of using the "/" key to toggle the Preserve Transparency option on and off for the selected layer.