There are two preferences panels that control the appearance of individual layers in the editing window. These are the "Colors" and "Layers" preferences (in menu File / Preferences..., "Display" section). Before explaining these commands, it is useful to understand the distinction between transparent and opaque layers in Electric.

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 both faster to draw and 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 stipple patterns are slower to draw, and because opaque color does obscure, the less common layers are drawn in this style. Drawing opaque layers takes less memory.

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.