Each layer has a color on the left and a pattern on the right. The color can be specified directly in the color picker, or it can be set to one of the transparent layers. If you change the color of a layer that has transparency assigned to it, the change will affects all layers assigned to that transparency.
You can draw in the pattern area to set a pattern, and you can choose from a set of predefined patterns by clicking on their image below the pattern-editing area. You can also choose an outline texture to draw.
The lower-right controls the appearance of the layer on the printed page. A separate "Use Fill Pattern" control lets you use patterns on a printer, even if they are not used on the display. The Opacity is also used for printer blending, and for some display algorithms.
When changing the background color, note that it must contrast with both the highlight color and the inverse of the highlight color (the inverse is black in the default settings).
After many changes to layer colors and patterns, you can restore the original state by pressing the "Factory Reset All Layers" button.
To save the trouble of hand-editing all of the colors, there are three predefined color schemes, available with the commands of the Window / Color Schemes menu:.