For Active and Inactive states, the System element will define the colors for all elements that do not have a specific color in the User Colors panel.
Your current color set is saved automatically when you exit Alias or switch to a different workflow (by choosing Default, Paint, Modeling, or Visualize from the Preferences > Workflows menu). You can have a different default color set for each workflow. Any additional color sets must be manually exported and imported using the File menu in the User Colors window.