For this you can simply use SugarCube's "tagged stylesheets" (see link for details), where you add particular tags you set up, to the passages you want colored differently. Then you add code to your Stylesheet section to color the passage based on those tags.
Hope that helps! :-)
P.S. In the future you can edit your question if you need to make changes to it (rather than adding an "answer"), and the Twine and story format information should go in the question tags. Thanks.