For now, yes you need to specify colors in the color scheme file. I would say you could also use entries there, but I would try to avoid changing those as...well...we all like the color schemes we are using already. I was hoping for a way to easily set the colors. As far as I have seen with the API though, you have to specify a scope to select a region. I'll probably go dive through some other plugins that do highlighting to see how they do it, as I'm hoping I just missed something. Let me know how it works though. I'm sure there are some bugs in it, but hey, learning experience right?
I'll try to check back to this post to see how things are going, but if there are issues, please create them on the project. I have a few things I know I need todo, but I'm sure it's not everything. Afterall, you know what functionality you are looking for!