To set properties for one or more polyfills, you will need to make sure that the Properties palette is displayed (Window > Properties), and that you have selected one or more polyfills with the Subselect tool (the polyfill regions will be outlined in red to indicate they are selected). This will make sure the PolyFill Properties are shown in the Properties palette.
To change the fill color of one or more selected polyfills, simply click on the color swatch (1) and select a color. If you want to restrict the color selection to only Web Safe colors, click the Web checkbox. For more on selecting colors and the purpose of the Web checkbox, see Selecting Colors.