Does there happen to be any way in the Alfresco theme to assign specific colors to various navigation buttons and possible pages? We are hoping to use colors to designate different areas of the website if possible (just a rough example: http://www.usatoday.com). Any information or feedback is appreciated.
Regardless of the theme this kind of modifications will require changes in the Razor view files. Basically you need to find a way to mark the various sections with different css classes and then style them accordingly. I think you will probably need to set different css styles based on categories, so you can use the current category id and set classes like these - currentCategory-1, currentCategory-2 etc. as the number will be the ID of the current category.
These are just some ideas that could be helpful but you need to figure out what would work best in your case.