Can't believe I am asking a simple question like this. Seems that PermissionsEx colors and prefixes only work with the addition of essentials, so is there a different plugin I can use to make the colors and prefixes show so I don't have to use essentials?
This is basically the functionality of the EssentialsChat side of it. You're looking for a chat manager plugin. I think there's one literally called ChatManager on BukkitDev you can find.