Clearspace uses a theming system that is actually quite powerful, but does require you to create .ftl templates for your pages. The themes can't be created from within Clearspace but they can be easily managed and applied almost any way you see fit. There is a document that describes the process and best practices for creating themes here: http://www.jivesoftware.com/builds/docs/clearspace/latest/ClearspaceThemingGuide.html
If you can't accomplish exactly what you want with themes, you will have to go more under the hood.
Using themes is probably the best way since for the most part it shouldn't interfere with upgrading.
Thanks for the pointer, it looks like this will let me do what I want to do. I had the impression when skimming the documentation that themes would not be an appropriate choice because they would be applied globally. Glad to see that's not the case!