The Layers Preferences (in menu File / Preferences..., "Display" section, "Layers" tab) controls the appearance of individual layers in the editing window.

Before explaining this panel, it is useful to understand the distinction between transparent and opaque layers.

Every layer in a technology is either transparent or opaque. Transparent layers are able to overlap each other, and it is possible to see all of them. Typically, the most commonly used layers are transparent because it is clearer to distinguish.

The remaining layers in a technology are opaque, meaning that when drawn, they completely obscure anything underneath. These layers typically have stipple patterns so that they do not cover all of the bits. In this way, the opaque layers can combine without obscuring the display. Because opaque color does obscure everything under it, the less common layers are drawn in this style.

When editing colors, the opaque layers have only one color, whereas the transparent layers have many different colors, considering their interaction with other transparent layers.