Use the Appearance panel to adjust the global colors, including background, foreground and accent colors for the composition. You can also adjust the colors for each voice in the Voices panel.
“Highlight color” is the color that the notes will be in when they are being played. If you don’t assign a highlight color, it will by default be a brightened color of the base color.
You can also turn on “Color notes by pitch” which will display options for you to choose a color for each pitch class.
Some color pickers have separate dark/light color fields with a chain icon between them. If the two colors are identical, they will be linked, and changing one will automatically update the other. Click on the chain icon to unlink the two colors, which will slightly darken the color for light mode so that they are no longer identical.