EDIT: Also, I just added that code, And that changes the colour to the subforums. I want to change the colours of the actual threads when they are read.
Change the default colors to what you want it to be when read, then style the unread ones differently. The software only adds classes on unread statuses.
Are you using a custom style? If so, it may be defined in a custom CSS (and using the !important tag) and if so, you will need to find it there. The code provided by @Brogan (and the unread one I did above which is identical) should work - as they work on all 3 of my forums that I have.
As @Brogan said, either is acceptable. I prefer using the EXTRA.css so that I can make other styles and copy the EXTRA.css info over and not have to worry about modifying the templates for each one.